MAIN Dialoge Mode Accessories - Striker menus: Table of Contents


MAIN User`s guide:Depp pages /Topical pages Last modified: 2-nov-2012

Depp pages /Topical pages

Main page: gate to tasks

"Depp pages" are cover topics of structure determination and analysis. They organized in two layers. The top layer, also reffered as the main depp page, contains menu items, which enable you to:

PROMPT

enter MAIN command "PROMT", where you can use MAIN command syntax interface and at the end also "QUIT" the working session.

DEPP_MAIN / Topical pages

The top layer menu block "DEPP_MAIN", enables you to choose specific topics and to load appripriate menu pages.

Top page menu names ( in yellow):

Topic of each Depp Page is covered or will be by one of the "General chapters on major topics" (../users_guide.HTML).

Molecular images

The items of the "MOL_IMAGE" menu block display the default image ("RE_IMAGE"), its symmetry mates ("SYMMETRY", "SYMM_CA"), generate surface "GEN_SURF" and provide link to rendring of the displayed objects ("PLOT").

SAVE_FILE

The items of the "SAVE_FILE" menu block save and restores the molecular model ("SAVE_FILE", "REST_FILE") and view ("SAVE_VIEW" and "REST_VIEW") and open the main configuration window ("MAIN_cfg")

Topical Pages of the DEPP_MAIN block

On the top of each "Depp Page" is the item "RETURN", which returns back to the "Top Depp Page".

MAPS page: electron density map calculation

See MAIN_DOC:calc_map/calc_map.html, MAIN_DOC:dens_mod/dens_mod.html,

For confuguring denisty modification tasks see MAIN_MENU:dens_mod.html.

TRACE page: model tracing from map

For overview see MAIN_DOC:build/new_struc.html.

The Depp page menu block trace.html carries the functionality. whereas the accompanying menu blocks allow you to gain control over the process and manually intrefere with automated density interpretation and model generation including model rebuilding.

Assisting menu block appearing on the page are

BLD_MAIN page: main chain model building and rebuilding

The page is there to assist yuo to build chain trace of molecules in traditional way - that is manually.

See MAIN_DOC:build/new_struct_manual.html.

BLD_RESI page: residue chain model building and rebuilding

See MAIN_DOC:build/build.html.

N_MOLECU page: cross molecule building, exchange and switching

MINIMIZE page: local minimization

VALIDATE page: structure validatation and analysis

See MAIN_DOC:analysis/analyze.html.

REFINE page: crystallographic refinement

See MAIN_DOC:refine/refine.html.

IMAGE page: displaying of molecular images

Most of the functionality of this page replaced by the "RE_IMAGE" tk_gui configuration tool. The only unique thing left is the surface generation.

After you have successfully loaded and displayed a molecular model (as described in MAIN_DOC:load_pdb/load_pdb.html MAIN_DOC:1mol/1mol.html)

See MAIN_DOC:mol_images/mol_images.html -although quite obsolete now.

SUPERIMP page: molecule superimposition

REN/SHOW page: rename and show of lists and names

UTILS page: utilities

MAP_MASK page: mask generation from map

MAIN User`s guide:All depp pages menu blocks Last modified: 24-feb-2007

All depp pages menu blocks

List of all menu blocks in alphabetical order. Not every block is assigned to a depp page, a few are present on several.

MAIN User`s guide:Structure and function of menu blocks

Structure and function of menu blocks

What is a menu block and what an item

A MENU BLOCK is a list of ITEMS separated by an empty space. Items within each block are displayed with the same color. Each ITEM is the visible string you actually see and can click. When clicked, a command line is submitted to the command sentence interpreter. Complex commands are written as macros.

Some items have filled or empty squares in front of them. This squares mark their status. Clicking on one of them usually does not result in anything, except the change of the mode reflected by the change of the box. Actions happen by clicking other (not-square-headed) related items within the same menu block, which use these modes as parameters.

Loading menu blocks

The file MAIN_CMDS_NEW:load_depp_page.com and MAIN_CMDS:load_depp_page.com (for the older releases) load the initial menu setup. MAIN_CMDS: and MAIN_CMDS_NEW:directories include macros of menu items (".cmds" files) and the "load_...com" files, which load the additional menu blocks. Each menu item command that starts with a "?" checks weather the file with that name is present in your working directory, and when found it is processed, otherwise the default MAIN installation file is taken.

If you want to create your menus, look at the "load" files as examples and see MAIN_COM:menu.html for further instructions.

Menu blocks documentation and documentation mode

Documentation files of menu blocks are stored in MAIN_MENU: directory and are accessible also via MAIN_DOC:dialog_manual.HTML.

When the "Depp pages" window is in the DOCUMENTATION mode, short description of the pressed BLOCK and ITEM is written to the standard output window. The DOCUMENT mode can be turned on or off either by pressing 'h' on the keyboard or by typing the command


> MENU DOCUMENT ON/OFF.

MAIN User`s guide:User program interactive communication File: communication.txt
Last modified: 24-feb-2007

User program interactive communication

There are three devices "mouse", "keyboard" and "dials" you can use to interact with the program once its is up and running.

MAIN creates three windows:

3D graphics window interactions

Mouse

The mouse can be used besides for picking atoms as a substitute input from dials.

It has 3 buttons: left (L), middle (M) and right(R). When one or two of them are pressed and moved, they replace input from the current dials set. By default:

The left button (L) can control rotations around X, Y and Z axis. When the cursor is moved within a circle of the image window center, the horizontal movements correspond to rotation about Y axis and vertical about X axis. If cursor is moved outside the circle, its' movement results in rotation about Z axis.

The middle button (M) controls translations along X and Y direction.

The left and middle button (LM) pressed together and moved vertically translate image along the Z direction.

The right button (R) controls scaling of the image (zoom). When cursor is moved towards the center of the image window, the image is shrunk, and when it is moving away from it, the image is expanded.

The right and middle button (RM) pressed together control clipping. When the cursor is moved towards the center of the image window, the clipping planes are moved together, and when it is moving away from it, the separation between the clipping planes is increased.

Changing dial definitions will also change the mouse button functions. In general, pressed middle button (M) mimics dials 1 and 2, pressed left and middle button (LM) mimic dial 3, right button (R) mimic dial 4, left button (L) mimics dials 5, 6 and 7, and combination of right and middle button (RM) mimic dial 8. (Dial numbering is two rows: 1-4, 5-8).

Releasing a mouse button while still moving the cursor results in a continuation repetition of the last move before the release. So smooth rotations of image on the screen can be achieved.

Mouse trouble shooting

When mouse doesn't behave properly it needs to be resetted. This happens quite often (on HP it is a rule) when the image window is iconized and then restored.

So reset the mouse by pressing any keyboard character key or type commands


> image mouse off
> image mouse on

If you get anoyed with dial rotations (you are unable to pick atoms because you keep moving the image), turn the mouse dial mimicking functions off:


> image mouse off

Keyboard shortcuts: magic of a keyboard touch

Pressing keys is usually the quickest way for an experienced user to issue commands. Keyboard single key shortcuts require no confirmation and are always at the tip of your fingers. They deal with image manipulation and they serve as shortcuts for some of the mostly applied clicks.

Currently these functions are supported:

Besides, each time a key is pressed, the mouse event mask is reset to avoid mouse events hangups due to Xwindows server client communication problems (bugs).

Arrow keys

The "arrow" keys mimic dials.

The yellow color shows to which pair of dials are arrow keys assigned.

Pressing "Home", "PgUp", "End", "PgDn" changes their assignment.

Dials

If you have them use them. They provide you with the best control of manual model building.

"Depp pages" window

You can select and trigger functions only with the mouse. The right mouse button clicks functions, the left one is reserved for future use to invoke configration windows.

Dials label window

It accepts no input. It only shows the current dial box and arrow key assignments.

User menu block communication

The arrow shape cursos indicates the program awaits new events from the interactive devices (mouse, dials and keyboard).

When an ITEM is clicked the cursor is changed from an arrow to a clock pointing that MAIN is executing the submitted commands. The arrow shape of the cursor reapears after the commands have been completed.

"help" mode is activated by pressing "H" in the image window and indicated by the cursor change into the question mark. When items are clicked in the help mode, their documentation is written into the terminal window and no command is submitted. Another "H" returns clicking of items into the working mode indicated by the "arrow" cursor shape.

Using menu items

Clicking a menu item always does something. A user is never asked for a confirmation, except in the case of deleting "active" atoms.

Arguments to items are hanging. They are always available (unless a list is empty). They are taken from:

The general philosophy is that you first define an argument and afterwards activate the function. This way the same argument can be reused in many functions, besides the argument list can be edited so that the atom clicked by mistake can be removed with no need to cancel the function. So approval of a command is not necessary. One level of "UN_DO" for coordinate changes can return the geometry of a model to its previous state.

Menu arguments: History list

Atoms are arguments. more precisely they become potential arguments, by clicking. When clicked, an atom is pushed on the top of the history list and a white label is displayed at the position of the atom. The last one clicked is always the first one on the list. The last atom can be dropped from the list ("HIS_DROP"). The whole history list can be cleared with "HIS_CLEA". The "HIS_DIST" allows you to measure and monitor interatomic distances when moving the atoms around. For more about history items see MAIN_MENU:history.html.

You can control the information displayed in the label. "IMAGE HISTORY" commands manipulate the history list and history functions. See MAIN_COM:image.html.

Menu arguments: Selection keys

The history list is created by clicking atoms. Atomic selections are usually created by providing history atoms to the "SELECT NICE" and "SELECT LONG" menu blocks. You can, however, at any moment choose to use the command language to define or redefine any of the keyed arguments. The most commonly used keys are "active", "passive" and ""image"".

Key "active" tells that something will happen with the selection of atoms (MINIMIZE, for example, will allow to move only active atoms). the key "image" contains the list of pickable atoms, ...

"KEY something SELECT ... END" commands manipulate the keys. See MAIN_COM:select.html.

There is also "WORK_REFL" key, which does not mark a list of atoms but reflections. It is a key, in contrast to "WORK_SEGM", which is a variable.

Menu arguments: inquired variables

Some arguments are inquired. You have to respond with a typed an answer, which can be either an integer or real number or a string. The resulting variables are either immediately applied ("LOAD_PDB") and also deleted after their use, or stored as GLOBAL variables to be used later in combination with other items ("MAP_ACT" and other map related menu items). Command


> show vari

reveals the current variable list and their values. For instructions how to set variables see "SET VARIABLE" in MAIN_COM:set.html.

Menu arguments: predefined variables

Some variables are defined in the initial macros as global variables and then used throughout the MAIN macros environment to pass some common arguments.

The variable "WORK_SEGM" contains a list of working SEGMENT NAMES. It is used to pass the list to various macros, which then use the list in their SELECT commands. "RE_IMAGE", "SYMMETRY", "REFINE" are only some of them. The variable is defined through "create_main_config.pl" tools in a "read.com" file and can be verified with "SHW_SEGM" updated with "UPD_SEGM" menu items. If the variable doesn't exist, or contains the wrong segment names, essentially nothing will work, unless you have created your own working environment.

In a "read.com" map variables "MAP_2FOFC", "MAP_FOBS" are defined in order to differentiate among various created maps.

The "DEF_ALL" variable is defined in a MAIN_UTILS:get_top_par_19_csd.com or similar script and it points to a macro, which assigns atom types and creates lists necessary for energy calculations.

MAIN Reference Manuals:ANALYSIS File: analysis.txt
Last modified: 18-jan-2003

ANALYSIS

Violations from ideal values as well as from the average are a measure of structure quality. The menu block "ANALYSIS" provide tools to map violations and deviations on 3D-image of a structure by utilizing color code. From blue, over red to yellow, dark blue being the best and yellow the worst. Seeing the whole spectrum means that distribution of deviations is continuous, whereas only a few colors mean that something should definitively be done with the model.

There are two pairs of modes ("GRP_RESI", "GRP_ATOM" and "BY_FORCE, "BY_ENERG") and two major kinds of analysis, B-value ("ANA_TEMP") and interaction energy ("ANA_ENER)". The results are displayed with the "ANA_IMAG"and centered on the worst (yellow) part"and centered on the worst (yellow) part.

The "ANA_BOND" and "ANA_ANGL" do not display but write to the terminal the statistics about deviations from each particular force field parameter term and the mean deviation for "BONDS" and "ANGLE" energy terms.

Use "ENERGY" menu block to switch on and off particular energy terms.

The menu block "ANALYSIS" is loaded with the file MAIN_CMDS:load_analysis.com.

GRP_RESI

When RESIDUE mode is on, interaction energy as well as B-value analysis are calculated on a residue basis (averaged over all atoms in a residue.)

GRP_ATOM

When ATOM mode is on, interaction energy as well as B-value analysis is performed and displayed for each atom.

ANA_TEMP

Performs a temperature factor (B-values) analysis.

MAIN_CMDS:anal_temp.cmds is the default macro.

BY_FORCE

The FORCE mode is the primary mode for energy analysis.

When the FORCE mode is on, energy of the structure is calculated only once and its derivatives are analyzed. The FORCE mode is particularly useful to spot bad contacts using the VdW energy term.

The FORCE mode does not make sense for analysis of electrostatics and density terms, where the direction of derivatives is important and not only its magnitude.

BY_ENERG

When the ENERGY mode is on, interaction energies for each atom or residue with the surrounding parts are calculated.

The ENERGY mode is the alternative for the FORCE mode. It can, however, be much more time consuming - particularly for calculation of non bonding interactions.

ANA_ENER

Performs the interaction energy analysis on atom or residue basis along the chain.

and displays color coded analysis on the screen.

MAIN_CMDS:anal_ener.cmds is the default macro.

The color codes of residues of your molecule are relative - from the lowest to highest value: blue means low values and yellow means high values. An equilibrated system should have the whole spectra. Especially bad are the yellow residues when the rest of color spectrum apart from blue is not present at all.

By default "AVERAGE" values are used for color coding. You can change this by using your own macro.

GEN_LIST

Configurable macro, which creates chosen top violators of analysis mode written into the macro "center_next.com" accessible by clicking "CENT_NEX" or using the keyword shortcut go "g". It is a user friendly way of doing the structure validation using the other analysis flags by the addiiton of sorting, top most violators and sigma cutoff.

This item will eventually replace all analysis menus.

ANA_BOND

ANA_BOND performs and writes the results of deviations of covalent BOND terms for the current force field parameters. At the bottom the overall deviations are shown. Use this to estimate the scale of the x-ray energy term (ENERGY DENSITY SCALE).

MAIN_CMDS:anal_param_bond.cmds is the default macro.

ANA_ANGL

ANA_ANGL similarly as ANA_BOND performs and writes the results of deviations of ANGLE terms for the current force field parameters. At the bottom the overall deviations are shown. Use this to estimate the scale of the x-ray energy term (ENERGY DENSITY SCALE).

MAIN_CMDS:anal_param_angle.cmds is the default macro.

MAIN Reference Manuals:AUTO_SEQ

AUTO_SEQ

Menu block "AUTO_SEQ" contains items, which try to recognize correct seqeunce and upon your approval replace it with the best guess.

Menu block "AUTO_SEQ" is loaded with MAIN_CMDS:load_auto_seq.com.

SEQ_FORW

Sets direction for sequence comaprison of the model with the protein sequence to "FORWARD". Sequences of model and protein will be compared along the current chain directions.

SEQ_REVE

Sets direction for sequence comaprison of the model with the protein sequence to "REVERSE". Sequences of model and protein will be compared in reverse chain directions.

SEQ_BOTH

Sequences of model and protein will be compared in both directions.

COMP_SEQ

Compares the residue sequence of the selected part of the model with the protein sequence found and prints the highest scores. When you find the correct sequence, go to "AUTO_SEQ" step.

AUTO_SEQ

Automatically renames residue names of the selected part of the model to the best match of the protein sequence found and builds the missing atoms. MAIN Reference Manuals:AUTO_STUFF File: auto_stuff.txt
Last modified: 17-jan-2003

AUTO_STUFF

Menu block "AUTO_STUFF" contains items, which do things, they are set for, automatically. User has to choose the range of a function application: working segment, key active or clicked history atoms.

Menu block "AUTO_STUFF" is loaded with MAIN_CMDS:load_auto_stuff.com.

FIX_PEPT

Redefines coordinates of the peptide bond between two clicked residues to ideal trans-peptide bond values. It fixes any mess that a minimizer run can not handle.

MAIN_CMDS:auto_stuff_fix_pept.cmds does it.

FLIP_PEP

Flips the clicked or selected peptide bonds for 180 degrees.

MAIN_CMDS_NEW:auto_stuff_flip_pept.cmds does it.

FIX_SIDE

Fixes a side chain conformation of chosen residues by looking for the nearest best conformation,

MAIN_CMDS:auto_stuff_side.cmds with the opion "ASIS does it.

EXT_SIDE

Fixes a side chain conformation of chosen residues by choosing the most extended conformation.

MAIN_CMDS:auto_stuff_side.cmds with the opion "EXTEND does it.

FIT_PEPT

Finds instantaneoulsy optimal peptide bonds orientation of selected "active" residues. The Algorithm checks non-bonding interactions with neighboring CA and CB atoms, secondary structure pattern and electron density map fit. All three terms are independently scaled and added together forming the scoring function.

The default macro MAIN_CMDS:auto_stuff_find_pept.cmds may need adjustment to your needs by a different "SECONDARY" scale and "MAP" assignment. By default the currently chosen map for contouring is used. Higher resolution gives higher scale to the density, while lower resolution maps are scaled down as carbonyls can not really be revealed by them, the non-bonding and secondary structure terms thus prevail.

The secondary structure pattern is recognized on the basis of CA and CB atoms of neighboring residues. Currently there are 7 possible secondary structure targets. Recognition process is absed on dihedral angle of four neighboring residues using CA atoms (CA-1234), dihedral angle of two adjacent two residues using CB-CA-CA-CB atoms and distances between 1-3 and 1-4 CA atoms. Standard values are shown below and can currently not be modified.


          B-anti  B-par   Alpha   3-10   Al-left  coll   p-pro
 CA-1234  178.7   177.5    49.8    71.1   -67.8  -82.5 -110.5
 CBA-CAB  178.7   178.4    71.1    80.4   -92.1 -123.1 -106.0
 CA 1-3    6.90    6.51    5.47    5.26    5.25   6.55   6.60
 CA 1-4   10.47    9.96    5.20    5.63    5.47   8.54   9.37

After recognizing a secondary structure target "CO" and "NH" groups are used to calculate dihedral energy terms with CA-CB or CA-CA atoms. The first two lines are used when "CB" atom is present in a residue, wheras neighboring "CA" atoms are used in the cases of a glycine.


 OC-CACB   77.4    55.4  -114.6   -75.6   -27.6   90.4   92.4
 HN-CACB  -81.7   -61.7     9.3   -13.7   117.5  -18.7  -22.7
 OC-CACA  -56.7   -81.9   111.7   147.2  -136.6  -64.9  -45.6
 HN-CACA   58.5   -82.3   114.7   102.8  -109.9  148.3  112.9

FIT_SIDE

Fits the side chain atoms into the density of the current active map.

MAIN_CMDS:auto_stuff_side.cmds with the opion "FIT does it.

RIG_RESI

"RIG_RESI" breaks residues into fragements as are rings, carboxylic and guanidinium groups and man chain and fits each of them into the active electron density map. After fit check the geometry and "minimize". Should be used with caution, because groups can move uexpectidly far away.

MAIN_CMDS:auto_stuff_rig_resi.cmds does it.

WEIGHTS

Defines weights of atoms by checking their positioning in a density map (MAP_2FOFC or MAP_FO). It starts with the root atom "CA" and proceedes along the main and side chain. The first atom outside the density contour leaves the rest of the chain weighted with 0 too.

Click on "RE_IMAGE" colors the regions outside the map with green.

The default macro is MAIN_CMDS:auto_stuff_weight.cmds which calls the actual automatic weighting procedure MAIN_UTILS:set_weight_auto_loop.com.

WEIG_ATO

Defines weights by considering the positions of individual atoms in the actiove density map. Weight 0 is set to atoms lating below the contour level, whereas the ones lying in the regions above or equal to the contour level is seto to 1.0.

Click on "RE_IMAGE" colors the atoms outside the map with green.

MAIN_CMDS:auto_stuff_weight_atom.cmds does it.

MAIN Reference Manuals:BUILD File: build.txt
Last modified: 28-Oct-96

BUILD

Enables the building of new residues into the model and replacement of existing ones. BUILD menu block is encoded into MAIN source.

"START", "ATTACH", "INSERT" and "CHANGE" are setup flags. Their mode is indicated with radio buttons. Only one is active at a time.

No action is undertaken as long as "RESID ??" is not pressed. Keyboard input is in the origin window (mono-screen).

The BUILD menu block is encoded into MAIN source.

START

START indicates that a new segment will start at the current image center position.

ATTACH

ATTACH indicates that the newly created chain will be attached to thge last clicked residue - assuming that the residues are part of the same kind of biopolymer.

INSERT

INSERT indicates that the new chain will start at the current image center position. However it will not be appended to the end of the atom records as by ATTACH, but INSERTED infront of the last clicked residue. A further CONNECT item click is needed to bring the chain to the desired place.

CHANGE

CHANGE means that the residue topology is supposed to be changed from the current one to the new one.

SEGMENT

SEGMENT provides the segment name of the newly created segment. If not provided the segment name increases by "1" each time a new chain is generated.

CHAIN

CHAIN provides a new chain name and a sequence root. Sequence root is a string of characters to which numbers are added when sequence ID is generated.

RESID ??

"RESID ??" requires input from keyboard: a list of residue names. Each residue may be preceeded by an integer number of its repetitions( e.g. "3 ALA CYS 2 MET ..."). MAIN Reference Manuals:BUILD_EXTEND File: build_extend.txt
Last modified: 20-Oct-97

BUILD_EXTEND

BUILD_EXTEND provides additional functions to BUILD block to enchance editing topology of the model.

"BUILD_EXTEND" menu block is loaded with MAIN_CMDS:load_build_extend.com.

DELE_ATOM

Deletes the last picked atom (MAIN_CMDS:dele_atom.cmds). NO confirmation is required!

DELE_RESIDUE

Deletes the last picked residue (MAIN_CMDS:dele_res.cmds). NO confirmation is required!

MERG_RES

Two consecutive residues (of the two last picked atoms) can be joined (MERG_RES) (MAIN_CMDS:merge_res.cmds). This should be applied when ATTACHING N and C terminals to a peptide chain. NTER and CTER are namely attached to a residue as a new residue that should be later on merged (joined) to the original one.

UPD_SEGM

Updates variable WORK_SEGM with segment names of all currently present atoms (MAIN_CMDS:update_segm.cmds)

SHW_SEGM

Shows the value of variable WORK_SEGM.


> show vari WORK_SEGM

When the variable WORK_SEGM does not exist or it does not contain the segment names you want, your interaction with the program through the menu items will almost certainly result in NOTHING.

CLONE

Clones the current "active" key atoms by making a copy and shifts them by a short distance. Useful during ab initio density interpretations when you simply want to apply the same topology a number of times (building beta strands or helical structures).

The macro is MAIN_CMDS:clone.cmds

Each time you have to provide (answer) with a new segment name and a sequence root.

Works well in combination with hydrogen bond constraints, when you for example "constrain" beta sheets arrangements with twist.

MAIN Reference Manuals:BUILD_MAIN File: build_main.txt

BUILD_MAIN

Last: modified: 24-feb-2007

The "BUIL_MAIN" is a merge of several menu blocks. It contains the most useful items of the "MODELER" menu block (modeler.html) merged with come others to enable smooth manual model rebuilding of the structure with no need to switch to other pages.

MOV_ATOM

Moves around the position of the last clicked atom.

Shortcut is "o".

MOV_RESI

Moves around the last clicked residue with the center of rotation on the last clicked atom.

Shortcut is "x".

MOV_SELE

Moves around atoms selected with the key active"with the center of rotation on the last clicked atom"rotation on the last clicked atom.

RT_BETWE

Rotates atoms between the last two clicked. Useful for peptide bond flipping.

RT_CHAIN

Rotates chain about all bonds between the last two clicked atoms.

Rotations about bonds in the rings are not allowed.

CON_CHAI

Connects two chains together by moving the fargment clickt first to the second fragment into a position suitable for covalent bond formation and builds the bond. (For example chains are connected at N-termnini).

INV_CHAI

Inverts the chain direction of the selected part by preserving the side chains on the same positions.

RE_ORDER

RE_ORDER changes the order of residues of the working segment ("WORK_SEGM") so that along the main chain covalently connected residues also follow each other.

The chain names and sequence IDs are automatically updated and changed.

OB_ACCEP

Accepts the current state of geometry changes imposed on the structure using manual rebuilding. It is an obligatory step following the "MOV_ATOM", "MOV_SELE", "RT_BETEE", "RT_CHAIN" and related functions.

Shortcut is "a".

OB_REJEC

Rejects the geometry changes by disengaging manual model building functions.

DIAL_INI

Initializes the dial set.

DIAL_RST

Resets the dial set to the lower on the stack of saved ones.

Useful when several manual buidling functions have been invoked simoultaneously and you want to switch between them. MAIN Reference Manuals:BUILD_RESI_AUTO File: build_resi_auto.txt

BUILD_RESI_AUTO

Last: modified: 30-mar-2007

The "BUILD_RESI_AUTO" fixes distrorted geometries (returns them to idela values) and fits fragemts of structure to electron density considering also some energy constrainst.

Positions of atoms of the "active" selection are modified.

FIX_PEPT

Sets all peptide bonds of selected atoms to trans by fixing bond length, angles and planarity.

FIT_PEPT

Fits peptide bonds of selected atoms to active electron density map considering also nonbonding interactions with CB atoms and secondary structure.

FLIP_PEP

Flips peptide bonds of selected atoms for 180 degrees.

EXT_SIDE

Sets geometry of side chains of selected atoms to all extended (trans).

FIX_SIDE

Sets geometry of side chains of selected atoms to closes rotamer as guessed from the dihedral angles.

RIG_SIDE

Fits fragments of residues of selected atoms to active electron density map as rigid bodies.

FIT_SIDE

Fits geometry of side chains of selected atoms to active electron density map considering also nonbonding interactions.

TRC_SIDE

Traces the side chains of selected residues by identifying residue with the best fit. It does not use any sequence information - only the restrainst of the active density map.

TRC_SIDE finds overalps and can close disulfides.

FIT_AUTO

Combines almost all above auto fitting features as well as density fitting under a single click. MAIN Reference Manuals:CENTER File: center.txt

CENTER

Last: modified: 20-nov-2007

In order to inspect your model systematically by progressing from one residue to the next, the "CENTER" menu block was created. The "CENT_NEX" item and the shortcuts for "go" ("g" and "G") lead you from one residue to the next.

There are two modes "BY_RESID" and "BY_VALID".

BY_RESID

"BY_RESID" mode enables you to jump from one residue to the next or previous in the sequence. It works in combination with "CENT_STA" and "CENT_DEF".

BY_VALID

"BY_VALID" mode enables you to jump from one atom on the list to the next one. It works in combination with "GEN_LIST".

CENT_STA

Sets the current center to the starting residue of the SEGMENT ID last clicked.

CENT_DEF

Sets the current center to last clicked one.

CENT_NEX

Jumpes to the next residue or atom on the list. When in "BY_RESID" mode the short cuts hve additional functionality "g" jumps forward and "G" backwards. In "BY_VALID" mode, shortcuts jump only forward to the next atom on the list.

GEN_LIST

It configures the validation, runs it on the "active" selection and jumps to the "BY_VALID" mode by assigning the atom center to the top most violator of the list.

Using the "configure" mouse button (right), the "create_anal_center.pl" script is invoked, which eanbles you to choose the things to be validated. Its "doit" results in creation of the local file "anal_center_list.cmds".

When using the "execute" mouse button (the left) the "anal_center_list.cmds" is executed. It writes the analysis of the active selection to the file "validate.dat", invokes its processing by the "analize_file.pl" and creates the "center_next.com" macro, which contains the sorted list of violators of your analysis. MAIN Reference Manuals:DEFINE File: define.txt
Last modified: 3-feb-1999

DEFINE

The "DEFINE" menu block has two purposes:

The method ("MTH_") and energy term only ("ONL_") items are switches. They are organized as a radio button menu groups (choosing one turns the other two off). Only one shitch cabn be active at a time. They specify the way the "DEF_" items act.

The items "DEF_INIT", "DEF_DELE", "DEF_APPE", "DEFINE" do some job create and modify the energy lists.

For command syntax you see MAIN_COM:define.html.

MTH_AUTO

When defining energy terms an automatic procedure ("active" atoms are used),

MTH_TOPO

When defining energy terms topology library residue description ("active" atoms are used).

MTH_ATOM

When defining energy terms the last atoms from the history lists are used editing the current "ONL_" energy term list. "BOND" take last two picked atoms, "ANGLE" three and "DIHEDRAL" and "IMPROPER" last four.

DEF_INIT

Before new terms are appended the particular list is initialized. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists.

DEF_DELE

All entries including the selected atoms are removed from the currently flagged energy term list. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists.

The most common use is in connection with "DEF_ATOM" and "DEF_IMPR", which allow you to choose an improper by clicking four atoms and remove all impropers that include these four atoms from the IMPROPER energy terms list.

DEF_APPE

New terms are appended to a flagged list. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists.

DEFINE

"DEFINE" actually invokes the macro to which "DEF_ALL" variable points to. Its only argument are the segment names included into the variable "WORG_SEGM". Applies to all energy terms and does not consider any of the provided DEFINE menu flags.

The "DEF_ALL" variable is "SET" in MAIN_UTILS:get_top_par_19_csd.com and points to the MAIN_UTILS:def_top_par_19.com macro.


> show vari DEF_ALL
> show var WORK_SEGM

ONL_CLAS

Only atomic CLASSES will be modified.

ONL_CHAR

Only atomic "CHARGES" will be modified. It should be barred in mind that this option applies only when used in combination with a topology library as data source ("DEF_TOPO").

ONL_BOND

Only the list of covalent "BOND" terms will be effected.

ONL_ANGL

Only the list of covalent bond "ANGLE" terms will be effected.

ONL_DIHE

Only the list of covalent "DIHEDRAL" angle will be effected.

ONL_IMPR

Only the list of covalent "IMPROPER" dihedral terms will be effected.

INQ_CLAS

"CLASSES" of all clicked atoms are set to the string typed in. Be sure that your history list contains only the atoms you want. If you feel uncertain use "HIS_ERAS" and click the atoms again.

MAKE_TOP

Creates (or recreates) the last entry in the topology library from the "active" key residues using the current energy lists.

For how to define the keys via menus see nice_sel.html and select.html , and MAIN_COM:select.html for mastering the "SELECT" command syntax.

For further reading see MAIN_DOC:top_par/top_par.html. MAIN Reference Manuals:DENS_MOD File: dens_mod.txt
Last modified: 21-jul-2007

DENS_MOD

Items of the menu block "DENS_MOD" invoke density modifications (solvent flattening and averaging) tasks ("RMS_FIT", "MAK_MASK", "DM_PREP", "DM_NEXT").

The local macros are created via "create" scripts. For setup explanation see MAIN_DOC:1mol/1mol.html and MAIN_DOC:nmol/nmol.html) and below.

For a more general scope of applications see also MAIN_DOC:dens_mod/dens_mod.html.

The menu is created with MAIN_CMDS:load_dens_mod.com.

RMS_FIT

Calculates all superposition matrices among all possible pairs of equivalent segments. The macro calculates rotation matrices and translation vectors, which superposition parametesr among all possible pairs of equivalent segments and "SAVE" results to files already in a form of a MAIN commands. These macros are used later in density averaging procedure to rotate the density maps.

Click invokes local macro "rms_fit.cmds".


 key ca sele atom name CA end
 rms coor all  eigen \
    sele ca .a segm name MOLA end \
    sele ca .a segm name MOLB end
 save over file mol_MOLA_to_MOLB.com rms

Macro is configured with "create_rms_fit.pl".

MAK_MASK

The macro checks for overlap between local and symmetry related neighbors and when appripriate reduces the atomic radii of touching atoms.

A file MAIN_DOC:nmol/make_masks.cmds contains a list of commands that are actually calls to MAIN_UTILS:make_atom_mask.com macro providing five parameters:


<?MAIN_UTILS:make_atom_mask "MOLA" 2 3.6 3 mask_MOLA.xmap

Macro is configured with "create_make_mask.pl".

DM_PREP

Generates the first map of electron density and copies it into map number 2, which serves as input for density modification procedures.

For example see MAIN_DOC:nmol/dm_prep.cmds.

Macro is configured with "create_dm_prep.pl".

DM_NEXT

Performs cycle(s) of density modification procedure as specified.

A call to a complete averaging cycle (loop) follows. There are four numbers.

For example see MAIN_DOC:nmol/dm_next.cmds and related macros.

The click invokes TWO macros configured separately "create_dm_next.pl" and "create_dm_loop.pl".

MAIN Reference Manuals:DEPP_MINI File: depp_mini.txt
Last modified: 24-feb-2007

DEPP_MINI

DEFINE

Defines atom classes andupdates energy lists of the atoms of the "WORK_SEGM" list of segmnet IDs.

KICK_??

Defines the maximal displacement of KICK for positions. The values up to 1.0A are still treatable by the minimizer.

KICK_ACT

Kicks coordinates of the "active" key by the maximal displacement of KICK specifed before. Default is 0.3A.

MINIMIZE

Minimizes the selected atoms using the "ON" energy terms.

MIN_BODY

Minimizes the selected atoms using the "ON" energy terms as a single rigid body.

MAIN Reference Manuals:PS_menu(PS300)

PS_menu(PS300)

DIAL_PS.TXT 7-MAR-93

EXIT

EXIT is used to EXIT the DIALOG mode and return to the


MAIN>.  It has no analog in command sentences. It is
possible to EXIT the DIALOG mode also by typing E on the keyboard.

MENU

IMAGE MENU ON

           OFF

MENU turns off MENU and makes the screen for molecular image larger. Menu can be obtained again by picking the area above the string MAIN displayed at the left top of the displayed viewport. Command sentences send to the main command interpreter are [IMAGE MENU ON] for getting menu to the screen and [IMAGE MENU OFF] for removing menu from the screen.

RE_DRAW

IMAGE OVER FALSE

RE_DRAW redraws the 3-dimensional objects (except MAP(s))

RE_MAP

IMAGE MAP OVER

RE_MAP redraws the MAP(s) centered at the current IMAGE CENTER.

STEREO

IMAGE STEREO ON

             OFF

STEREO toggles the STEREO ON or OFF.

PLOT


> inquire file_name "PLOT FILE NAME:"
> open unit 99 file file_name write_enable
> image unit 99 plot on initialize
> image over false map over
> image plot off
> close unit 99

Creates a plot file of the current IMAGE. The name of the plot file is INQUIRED by the prompt "PLOT FILE NAME" and should be typed in.

CENTER

IMAGE CENTER ATOM int1

Centers the image to the position of the last picked atom.

History

An atom is PICKED, when the cursor is placed on its IMAGE location and a mouse button is pressed.

HIS_ERAS

IMAGE HISTORY INITIALIZE

HIS_ERAS empties the history array (set the counter of atoms present to zero and deletes all history images).

HIS_DROP

IMAGE HISTORY DROP

Drops the last PICKED atom from the HISTORY list.

!5 HIS_CONT !HISTORY CONTINUE ON / TRUE ! OFF / FALSE ! !Toggles the HISTORY CONTINUE flag ON or OFF. It's used when !HISTORY DISTANCE, ANGLES or DIHEDRALS are displayed. When !the CONTINUE flag is OFF only the last 2/3/4 picked atoms !are used to display the history distance, angle or dihedral. !When the CONTINUE flag is ON all distances, angles or !dihedral angles among consecutive atoms in history list are !displayed.

HIS_DIST

IMAGE HISTORY DISTANCE

Displays DISTANCE among last two PICKED atoms and connects them with the white history line.

HIS_ANGL

IMAGE HISTORY ANGLE

Displays the ANGLE among the last 3 PICKED atoms and connects them with the white history line.

HIS_DIHE

IMAGE HISTORY DIHEDRAL

Displays the DIHEDRAL angle among the last 4 PICKED atoms and connects them with the white history line.

HIS_INTE

IMAGE HISTORY INTERNAL

Displays DISTANCE, ANGLE and DIHEDRAL information of last 4 PICKED atoms. The CONTINUE flag does not affect displaying of internal coordinate information.

HIS_NEIGH

IMAGE HISTORY NEIGHBOUR his_neigh

Finds the NEIGHBOURS of the last PICKED atom. The neighbours are atoms closer than the specified distance real, at least 3 covalent bonds away from the last picked atom and are included in the key 'image'. The distance criterion is stored in the variable name 'his_neigh'. The default value is 4.0A and can be SET with a


MAIN> SET VARIABLE his_neigh  real

command sentence and its value can be SHOWN with a


MAIN> SHOW VARIABLES his_neigh

HIS_RAMA

IMAGE HISTORY RAMACHANDRAN

HIS_RAMA sets a cross into Ramachandran plot when it is displayed as part of the GRAPH object number 1. It is enough to PICK any atom of the desired residue and then hit HIS_ARMA. The program finds the required atoms alone (-C N CA C +N).

Modeling

The modeling functions (RT_ANGLE, RT_CHAIN, RT_DIHED, ROTATE, TRANSLATE, ROT_TRAN, MOV_DIST, MV_6_INT) activate OBJECTS for interactive spatial modifications of molecular geometry and assign DIALS to them. After activating an OBJECT the IMAGE has to be redrawn (RE_DRAW). Most of them consist of more than one command sentence or even call some external command files. (So don't get confused when looking into the file INPUT.COP). The required data are transferred to the command files via MAIN VARIABLES.

RT_ANGLE


>SET VARIABLE iatom1 int1 VARIABLE iatom2 int2 VARIABLE iatom3 -
  int3 VARIABLE iobj1 int4]
>@MAIN$U:ANGLE.ROTA

Defines an ANGLE OBJECT. Takes the last 3 atoms from the HISTORY list.

RT_DIHED


> SET VARIABLE iatom1 int1 VARIABLE iatom2 int2 VARIABLE iatom3 -
   int3 VARIABLE iatom4 int4 VARIABLE iobj1 int5
> @MAIN$U:DIHED.ROTA]

Defines a DIHEDRAL OBJECT. Takes the last 4 atoms from the HISTORY list.

RT_CHAIN

RT_CHAIN activates rotation of all BONDS between the last 2 PICKED atoms. When the chain is to long or there are rings in the system OB_REJECT should be done by the user in order to avoid possible misdefinitions. MAIN is able to checking only each separate bond rotation. When there are more bonds to be rotated in the chain and one is not allow to rotate, some error messages will appear.

RT_CHAIN calls in a loop a variety of command files, for each rotatable bond one. After each 8th bond, the DIAL WRITE sentence is automatically done. The last DIAL definition should be saved by the user in order to keep it on the DIAL definitions stack.

MOV_DIST


> SET VARIABLE iatom1 atom-num1 VARIABLE iatom2 atom-num2
 VARIABLE iobj1 inte
> MAIN$U:BOND.DIST

Moves (translates) the molecule of the last PICKED atom. in the direction of the vector connecting the last two PICKED atoms.

MOV_RT_6

Activates 3 BOND and 2 ANGLE rotations and 1 DISTANCE movement. It is the INTERNAL (relative) coordinate way of the ROTATION and TRANSLATION (ROT_TRAN) function that is applied in absolute (cartesian) coordinate space. The 6 last PICKED history atoms are required. The DIAL set is saved automatically.

ROTATE

ROTATES the molecule of the last PICKED atom around the last picked atom.

TRANSLATE

TRANSLATES the molecule of the last PICKED atom.

ROT_TRAN

Combines ROTATION and TRANSLATION of the molecule of the last PICKED atom. The center of rotation is defined at the position of the last PICKED atom. The DIAL set is saved automatically.

INV_CHIR


> SET INVERSE atom-num1 atom-num2

Interchanges the positions of the 2 side chains attached to a single atom. In other words: inverses chirality of the common neighbour of the last 2 PICKED atoms.

Dials

Controls the DIAL definitions.

DIAL_INI

Set dials to their INITIAL (default) definition. (image center translation, scaling, rotation and clipping)

DIAL_BCK

Makes a backup of the current DIAL definition to the memory.

DIAL_RST


> SET DIAL 1 WRITE

Restores a DIAL set definition from the memory and increases current dial set counter for one.

DIAL_VIE


> SET DIAL 1 VIEW

Assigns DIALS to VIEW parameters as scaling of screen, stereo angle, distances from viewer position to the center, character scale.

DIAL_DRO

Drops all of saved (backuped) DIAL sets from the memory and initialize dials.

Objects

OB_START


> OBJECT int SET INIT

OB_REJEC


>OBJECT int SET TRUE

OB_ACCEP


>OBJECT int SET FALSE

These commands affect all activated OBJECTS. They are either returned to their initial position (OB_START) or reject the changes completely (OB_REJEC) or accepts (OB_ACCEP) them and change the atom coordinates. By OB_REJEC and OB_ACCEP the complete image is redrawn.

Delete_and_make

BON_DELE


> DELETE BOND atom-num1 atom-num2

A covalent BOND between the last 2 PICKED atoms can be DELETED or created (JOIN).

BON_MAKE


> JOIN atom-num1  atom-num2

A covalent BOND between the last 2 PICKED atoms can be DELETED or created (JOINED).

!BON_INCR increases order of a bonds (creates a double bond out of a single one) !BON_DECR decreases order of a bonds (creates a single bond out of a double one)

ATO_MAKE


> make atom coordinate 3*real
> image color 222 select atom number atom-num1 end atom cross

MAKES an ATOM with the name X at the current image CENTER position and displays it as a CROSS.

ATO_DELE


> delete atom select atom number atom-num1 end

DELETES the last PICKED atom. Since this is a very risky operation the user is asked once more to confirm the DELETION.

PAIR_MAK


> make pair atom-num1 atom-num2

MAKES a PAIR from the last 2 PICKED atoms.

MAIN Reference Manuals:DIALS File:>doc/menu/dials.txt
Last modified: 14-nov-95

DIALS

Enables you to perform the basic control of DIAL set definitions. (See also SET DIALS in reference manual.)

Current dial set definition is echoed in the Dials window in the lower left corner.

DIAL_INI

Set dials to their INITIAL (default) definition. (image center translation, scaling, rotation and clipping)

DIAL_SAV


> SET DIAL 1 WRITE

Saves the current DIAL set as the last one on the dial sets stack. (30 dial sets can be saved.)

DIAL_RST


> SET DIAL 1 READ

Restores a DIAL set definition and increases current dial set counter for one. Repeating hits allow you to sroll through entire set of saved dial set definitions.

DIAL_VIE


> SET DIAL 1 VIEW

Assigns DIALS to VIEW parameters as scaling of screen, stereo angle, distances from viewer position to the center, character scale (for PHIGS only).

DIAL_DRO

Drops all of saved DIAL sets from the memory and initialize dials.

MAIN Reference Manuals:DISPLAY_LONG File: display_long.txt
Last modified: 27-sept-94

DISPLAY_LONG

The DISPLAY_LONG menu BLOCK controls basics of the image re-processing and interaction with a user.

EXIT

EXIT is used to EXIT the DIALOG mode and return to MAIN>. It has no analog in command sentences. When CRYSTAL eyes STEREO screen is turned on, picking EXIT turns STEREO OFF and returns control to the mono screen.

Keyboard equivalent keys are 'e' and 'E'.

MENU


> IMAGE MENU ON
             OFF

MENU turns off MENU and expands the molecular image to the whole MAIN window size. The menu can be retrieved again by picking the item MENU once more.

Keyboard equivalent is key 'M'.

RE_DRAW


> IMAGE OVER FALSE

RE_DRAW redraws all 3-dimensional objects (except MAP(s)) stored in the program. Background IMAGE objects are not redrawn.

Keyboard equivalent is key 'r'.

RE_MAP

Keyward: map redraw, recontour


> IMAGE MAP OVER

RE_MAP redraws all MAP(s) centered at the current IMAGE CENTER.

Keyboard equivalent is key 'r'.

STEREO


> IMAGE STEREO ON
              OFF

STEREO toggles the STEREO ON or OFF.

Keyboard equivalent is key 's'.

PLOT


> inquire file_name "PLOT FILE NAME:"
> open unit 79 overwrite file file_name
> image unit 79 plot on initialize
> image over false map over
> image plot off
> close unit 79

Creates a plot file of the current IMAGE. The name of the plot file is INQUIRED by the prompt "PLOT FILE NAME" and should be typed in.

GRAPH objects can not be PLOTTED this way!

CENTER


> IMAGE CENTER COORD 3*real

Centers the image to the current position of the last picked atom.

Keyboard equivalent is key 'c'.

MAIN Reference Manuals:DISPLAY_SHORT File: display_short.txt
Last modified: 27-sept-94

DISPLAY_SHORT

DISPLAY_SHORT consist of 3 items from the DISPLAY_LONG: MENU, STEREO and CENTER.

MAIN Reference Manuals:ENERGY

ENERGY

Is used to turn separate ENERGY flags ON and OFF.

MAIN Reference Manuals:HBONDS File: hbonds.txt
Last modified: 3-oct-96

HBONDS

HBONDS commands enable you to manipulate the list of hydrogen bonds. If you want to display them, you have to bare in mind that the macro 're_image.cmds' is the place to govern presentation of hydrogen bonds on a display.

They are useful during minimization as they preserve as well as enforce (regular) hydrogen bonding patterns.

The macro is loaded using MAIN_CMDS:load_hbonds.com.

HBON_WORK

HBON_WORK calculates the list of hydrogen bonds for the "WORK_SEGM" list of segmnet IDs.

HBO_WORK

HBON_WORK calculates the list of hydrogen bonds for the "WORK_SEGM" list of segmnet IDs.

HBO_MAIN

HBO_MAIN calculates the list of hydrogen bonds for the main chain atoms of the "WORK_SEGM" list of segment IDs.

HBON_DEL

HBON_DEL deletes the hydrogen bond between the two last picked atoms.

HBON_CLEAR

HBON_INI initializes the hydrogen bond list by deleting all hydrogen bonds.

MAIN Reference Manuals:HISTORY File: history.txt
Last modified: 27-sept-94

HISTORY

Picked atoms constitute the HISTORY list. An atom is PICKED, when the cursor is placed on its IMAGE location and a mouse button is pressed. The history information of the picked atom appears in white at the atom position.

HISTORY list is input for any other Strikes MENU function. In general atoms are first picked in desired order and then some other function is activated. This way mistakes by picking atoms can be corrected easily and the same picked atoms can be reused.

Through the HISTORY lists of interatomic distances, angles, dihedral angles or ramachandran plot position of a amino acid can be monitored while changing atom(s) positions.

HIS_ERAS


> IMAGE HISTORY INITIALIZE

HIS_ERAS empties the history array (set the counter of atoms present to zero and deletes all history images).

HIS_DROP


> IMAGE HISTORY DROP

Drops the last PICKED atom from the HISTORY list.

Keyboard equivalent key is 'd'.

HIS_NAME


> IMAGE HISTORY NAME ON
                     OFF

HIS_NAME removes the HISTORY atom information from the image without actually modifying the history list. Toggling the atomic history list is usefull when it gets large.

HIS_DIST


> IMAGE HISTORY DISTANCE

Displays DISTANCE between last two PICKED atoms and connects them with the white history line.

HIS_ANGL


> IMAGE HISTORY ANGLE

Displays the ANGLE among the last 3 PICKED atoms and connects them with the white history line.

HIS_DIHE


> IMAGE HISTORY DIHEDRAL

Displays the DIHEDRAL angle among the last 4 PICKED atoms and connects them with the white history line.

HIS_INTE


> IMAGE HISTORY INTERNAL

Displays DISTANCE, ANGLE and DIHEDRAL information of last 4 PICKED atoms.

HIS_NEIGH


> IMAGE HISTORY NEIGHBOUR his_neigh

Finds the NEIGHBOURS of the last PICKED atom. The neighbours are atoms closer than the specified distance, at least 3 covalent bonds away from the last picked atom and are included in the key 'image'. The distance criterion is stored in the variable named 'his_neigh'. The default value is 3.6A and can be SET with a


MAIN> SET VARIABLE his_neigh  real

command sentence. Its value can be displayed with


MAIN> SHOW VARIABLES his_neigh

HIS_RAMA


> IMAGE HISTORY RAMACHANDRAN

HIS_RAMA draws a cross into Ramachandran plot when it is displayed as part of the GRAPH object number 1. It is enough to PICK any atom of the desired residue and then hit HIS_RAMA. The program finds required atoms atomatically (-C N CA C +N). MAIN Reference Manuals:HISTORY_FLAGS

HISTORY_FLAGS

Turns ON and OFF flags for HISTORY record constituents (atom, residue names and numbers, ...).

MAIN Reference Manuals:IMAGE

IMAGE

Menu blocks for molecular images creations and modifications are loaded on page 6. After you have successfully loaded and displayed a molecular model (using a kind of MAIN_DOC:1mol/read.com macro, "LOAD_PDB" item from the menu page 7 utils.html menu block or some other way),

MAIN Reference Manuals:IMAGE_COL File: image_col.txt
Last modified: 20-jan-98

IMAGE_COL

The IMAGE_COL menu block items specifies the color mode (COLO_SET) or colors to be applied in the subsequent IMAGE or COLOR atom commands.

The explicit colors "WHITE", "PINK", "RED", "ORANGE", "YELLOW", "GREEN", "GREEN_DA", "BLUE_LIG", "BLUE_DAR" define an color by index using MAIN_CMDS:image_color.cmds macro, where as the "COLOR_?? enables a user to provide his own color index through macro MAIN_CMDS:image_color_ask.cmds.

The IMAGE_COL menu block is loaded with the file MAIN_CMDS:load_image_col.com.

MAIN Reference Manuals:IMAGE_COL2 File: image_col2.txt
Last modified: 20-jan-98

IMAGE_COL2

The IMAGE_COL2 menu block items color selected atoms using a particular property. All items switch the SET COLOR mode on.

The IMAGE_COL2 menu block is loaded with the file MAIN_CMDS:load_image_col2.com.

COL_DEFA

Sets the color of the "display" atoms to their default values (MAIN_CMDS:image_col2_default.cmds).

COL_CURR

Sets the color of the "display" key atoms to the last specified color (MAIN_CMDS:image_col2_current.cmds).

COL_CARB

Sets the color of the "display" key atoms to the last specified color (MAIN_CMDS:image_col2_carbons.cmds).

COL_RESI

Sets the color of the "display" key atoms according to their amino acid residue type (MAIN_CMDS:image_col2_by_resi.cmds).

COL_WEIG

Sets the color of the "display" key atoms according with their crystallographic WEIGHT (occupancy) (MAIN_CMDS:image_col2_by_weight.cmds).

MAIN Reference Manuals:IMAGE_DATA File: image_data.txt
Last modified: 20-jan-98

IMAGE_DATA

The IMAGE_DATA items relate to atomic RADII sizes and Connolly surface generation.

The IMAGE_DATA menu block is loaded with the file MAIN_CMDS:load_image_data.com.

RAD_VDW

Sets radii of "display" atoms to VdW radii, whatever their values in MAIN are.

You can check them with command


> show radi sele display end

RAD_*0.5

Multiplies the radii of "display" atoms with 0.5. Clicking it twice you get a quarter.

RAD_??

Enables you to radii of "display" atoms to your value of your choice (MAIN_CMDS:image_data_rad.cmds).

GEN_SURF

Generates Connolly surface with the default density of 5 points per sqare A (MAIN_CMDS:image_gen_poin_surf.cmds). MAIN Reference Manuals:IMAGE_DO File: image_do.txt
Last modified: 20-jan-98

IMAGE_DO

The IMAGE_DO menu block items really "do" something with the image, their either erase it, bring molecular and map images on the display or save the view and and image commands for future editing of macros.

The IMAGE_DO menu block is loaded with the file MAIN_CMDS:load_image_do.com.

ERASE

ERASES the current image.

BONDS

Creates a bond image of the "display" atoms.

ATO_CROS

Creates an atom cros image of the "display" atoms.

ATO_NAME

Creates an atom name image of the "display" atoms.

RES_NAME

Creates an residue name image of the "display" atoms.

SEQUEN

Creates an sequence IDs image of the "display" CA atoms.

STICKS

Creates an bond stick image of the "display" atoms.

ATO_BALL

Creates an atom ball image of the "display" atoms.

CHAIN_TR

Creates a chain trace image of the "display" protein atoms.

SURFACE

Creates a Connoly surface image the "display" atoms.

SAV_VIEW

Saves the current view into the specified file (MAIN_CMDS:image_do_save_view.cmds).

BEG_MACRO


(MAIN_CMDS:image_do_beg_copy.cmds).

END_MACRO


(MAIN_CMDS:image_do_end_copy.cmds).





MAIN Reference Manuals:IMAGE_LIGHT

File: image_light.txt
Last modified: 9-dec-97

IMAGE_LIGHT

The IMAGE_LIGHT block items provide interactive lights (1-4) control.

The menu is loaded with the file MAIN_CMDS:load_image_light.com.

It uses two macros. MAIN_CMDS:image_light_mode.cmds switches among modes. The radio buttons indicate which mode will be applied.

MAIN_CMDS:image_light_funct.cmds invokes the chosen function (by mode status variable) on the specified light (LIGHT_1 to 4). Clicking this buttons can change the light status and definitions.

TURN_ON

Turns the light on mode.

TURN_OFF

Turns the light off mode.

DIALS

Turns the dial light manipulation mode. The dials can manipulate a light COLOR, DIRECTION angles, DISTANCE and distance ATTENUATION parameters.

AMBIENT

Turns the AMBIENT light mode. An ambient light comes from all directions. It has only COLOR parameters.

DIRECTIO

Turns the DIRECTION light mode. An directional light comes from a defined direction. It has COLOR and DIRECTIONAL parameters.

POSITION

Turns the POSITIONAL light mode. A positional light comes from a defined position. Light is spreaded in all directions. The light has COLOR, DIRECTION and DISTANCE and distance attenuation parameters. (Direction and distance define a position.)

SPOT

Turns the SPOT light mode. An SPOT light is a directional light which shines in a cone. It has therefore two attenuation paramaters, a distance and angle.

LIGHT_1

Applies the chosen mode function to the light 1.

LIGHT_2

Applies the chosen mode function to the light 2.

LIGHT_3

Applies the chosen mode function to the light 3.

LIGHT_4

Applies thechosen mode function to the light 4.

SHOW

Shows the current status of the lights and their parameters (color, direction, distance, kind).


> show image light





MAIN Reference Manuals:IMAGE_MAP

File: image_map.txt

IMAGE_MAP

Last Modified: 24-jan-97

"IMAGE_MAP" menu block enables you to create and modify images of maps. Complete block appears on the page 6.

The IMAGE_MAP menu block is loaded with the command "<MAIN_CMDS:load_image_map.com". It includes some default variable setups as active map (1), box sizes (12 grid points) and contouring level (1.0). These values can be later modified with the MAP_ACT?, MAP_BOX and MAP_CONT.

See also the "IMAGE MAP" commands in MAIN_MENU:image.html.

MAP_ACT?

Defines active map (MAIN_CMDS:make_map_active.cmds).

MAP_CONT

Defines the contourting level for a map presenation.

MAIN_CMDS:image_map_contour.cmds

MAP_BOX

Defines box in grid frm the center in which the active map will be drawn.

MAIN_CMDS:image_map_box.cmds

MAP_ON

Enable active map re_drawal (using "RE_MAP" item or pressing "r").

MAIN_CMDS:image_map_on.cmds

MAP_OFF

Disables active map re_drawal. The image stays as it is, it can however still be included or removed from the display list.

MAIN_CMDS:image_map_off.cmds

MAP_LINE

Creates a line presentation of map, contoured along X, Y and Z axis,

MAIN_CMDS:image_map_lines.cmds

MAP_STIC

Creates stick presentation of map.

MAIN_CMDS:image_map_sticks.cmds

MAP_X-AX

Draws lines or sticks along X-AXIS.

MAIN_CMDS:image_map_x-ax.cmds

MAP_Y-AX

Draws lines or sticks along Y-AXIS.

MAIN_CMDS:image_map_y-ax.cmds

MAP_Z-AX

Draws lines or sticks along Z-AXIS.

MAIN_CMDS:image_map_z-ax.cmds

MAP_AREA

Creates a polygonal surface presentation of the active map.

MAIN_CMDS:image_map_area.cmds

SHOW_MAP

The information about the active map.

MAIN_CMDS:image_map_show.cmds

MAP_MASK

Creates a mask (envelope) around the "active" atoms using a cushion of 5 grid points around the currently active map "MAP_ACT?".

The default mask creation method is based on the assumption that atoms lie within peaks of electron density and that their density spreads as long as the gradient is down hill. As soon as it goes up it is assumed that such grid points belong to some other peak.

The macro MAIN_CMDS:image_map_mask.cmds contains the commands.

MAIN Reference Manuals:IMAGE_COL

IMAGE_COL

MAIN Reference Manuals:IMAGE_MENU

IMAGE_MENU

The functions of the Bottom_menu are activated when an IMAGE object is picked. The available commands only set modes.


> image remove inte1 (inte2)
> image include inte1 (inte2)
> set dial inte1 color inte2 string
> set dial inte graph text string

COLOR

COLOR sets the color mode. When an image object will be picked, two dials will be connected to its COLOR ( hue and saturation).

TEXT_TRN

TEXT-TRN sets the text translate mode When a GRAPH text object will be picked, translation of the string will be connected to the dials.

INCL_REM

INCL_REM sets the include and remove mode ONE sets one picked object mode TWO sets two picked object mode (first and the last) When ONE is active, the picked image object will be included or removed from the display list. When TWO is active, 2 image objects should be picked in order to include or remove all objects from the first to the second picked one from the display list.

MAIN Reference Manuals:IMAGE_SEL File: image_sel.txt
Last modified: 20-jan-98

IMAGE_SEL

The IMAGE_SEL menu block items define the key "display" which is used in subsequent image commands via the menu block "IMAGE_DO" (image_do.html) and set color commands via the menu blocks "IMAGE_COL" (image_col.html) and "IMAGE_COL2 (image_col2.html).

The "ACT_" items actually share the menu block NICE_SEL macros (nice_sel.html) for key "active manipulation.

The IMAGE_SEL menu block is loaded with the file MAIN_CMDS:load_image_sel.com.

USE_WORK

All atom sfrom the current "WORK_SEGM" are assigned to the key "display".

Copies the contents of the key "active" to the key "display" (MAIN_CMDS:image_use_active.cmds). MAIN_CMDS:image_use_work.cmds

USE_ACTI

Copies the contents of the key "active" to the key "display" (MAIN_CMDS:image_use_active.cmds).

USE_HIST

Defines the whole history list (all clicked atoms) to the key "display" (MAIN_CMDS:image_use_history.cmds).

NOHYDROG

Removes hydrogen atoms from the key "display".

RES_NAME

Redefines the key "display" by selecting all residues with the same residue name as all clicked atoms being part of the history list (MAIN_CMDS:image_use_by_res_name.cmds).

EACH_TEN

Redefines the key "display" by selecting each tenth CA or P atom for proteins and nucleic acids respectively (MAIN_CMDS:image_use_each_ten.cmds).

ACT_SEGM

Selects the atoms of the last clicked molecule (MAIN_CMDS:sel_active_segm.cmds).

ACT_2RES

Selects the residues between the last two clicked atoms (MAIN_CMDS:sel_active_2res_rang.cmds). Residues do not need to be a part of the same molecule or segment.

ACT_NEIG

Select atoms within a certain number of covalent bond steps from the last clicked atom (MAIN_CMDS:sel_active_neigh.cmds).

ADD_MODE

Switches between the ADD_MODE ON (MAIN_CMDS:sel_add_mode_on.cmds) and OFF (MAIN_CMDS:sel_add_mode_on.cmds).

MAIN User`s guide:Magic of a keyboard touch File: keyboard.txt
Last modified: 21-oct-2012

Magic of a keyboard touch

Pressing keys is usually the quickest way for an experienced user to issue commands. Keyboard shortcuts require no confirmation and are always at the tip of your fingers.

There are single and multiple key shortcuts.

Single key shortcuts

Currently these functions are supported:

  • '+' rotates the image for the stereo angle in the + direction,
  • '-' rotates the image for the stereo angle in the - direction,
  • 'M' toggles the image menu on and off,
  • 'a' accepts geometry of currently defined active objects,
  • 'b' rigid body fit to map of groups of fragments ("RIG_SIDE"),
  • 'c' or 'C' sets the current rotation to the last picked atom,
  • 'd' or 'D' drops the last picked atom from the history list,
  • 'e' or 'E' exits the dialog mode, MINIMIZation and REFINEment,
  • 'f' flips peptide bond or side chain of the last picked atom,
  • 'g' go to the next residue: a shortcut to "CENT_NEX",
  • 'h' toggles menu documentation mode on and off,
  • 'j' do auto fitting job: a shortcut to "FIT_AUTO",
  • 'k' kick "active" atoms: a shortcut to "KICK_ACT",
  • 'l' selects the last clicked residue: a shortcut to "ACT_LAST"
  • 'm' minimizes the "active" key selection of atoms:: a shortcut to "MINIMIZE",
  • 'n' selects the neighboring atoms: a shortcut to "ACT_NEIG",
  • 'o' move the last clicked atom: a shortcut to "MOV_ATOM",
  • 'p' peptide fixes: a shortcut to "FIX_PEPT" and "FIT_PEPT" together",
  • 'r' or 'R' redraws the maps around the current center,
  • 's' or 'S' toggles stereo on and off,
  • 't' togless"TETHER"optimization on/off: a shortcut to"UN_DO",
  • 'u' undo the last coordinate change: a shortcut to"UN_DO",
  • 'w' calls a macro as defined by character variable"WORK_MACRO",
  • 'x' move the last clicked residue: a shortcut to"MOV_RESI",
  • 'z' fit side chains of the last clicked residues to density: a shortcut to"FIT_SIDE",
  • '1' to '0' includes or removes maps (1 to 10) from the image (since 10 is no key 0 is used instead)"(since 10 is no key 0 is used instead).

Besides, each time a key is pressed, the mouse event mask is reset to avoid mouse events hangups due to Xwindows server client communication problems (bugs).

Multiple key shortcuts

Menu items on the currently displayed menu page can be called by the sequence of 3 keys. The sequence must begin with CTRL or ALT keys followed by two characters. The first character is matched against the first character of a menu item, whereas the second is matched against the character following the "_" sign. When the "_" is absent, then the second character is mached. In the case a unique menu item is identified it is invoked as is clicked on.

The "CTRL" key sequence invokes the item, whereas the "ALT" key invokes its configuration GUI. MAIN Reference Manuals:KICK_STUF File: kick_stuf.txt
Last modified: 6-jun-2002

KICK_STUF

The "KICK_STUFF" menu block is loaded with the "MAIN_CMDS:load_kick_stuff.com" macro.

KICK_0.3

Kicks sizes from "0.1" to "0.4" A are adjusted with "KICK_0.x" items.

KICK_??

You can specify your own value by clicking the "KICK_??" item. Maximal value for refinement actually is 0.33. With higher kicks you may distort the structure to the level which will prevent the minimizer to converge to reasonable geometry (bond angles may cross the bonds and the minimizer can not get them back due to the 180.0 deg problem).

KICK_SEE

The "KICK_SEE" sets the seed for the random number generator. After each KICK the seed is increased by 1 automaticaly.

MAP_+_??

Specified the number of maps you wish to average. By default the number is 1 - so the maps are only calculated. Averaged maps allow use of kicks up to 1.5 or even 3.0 A (resolution and number of cycles dependent).

The macro is MAIN_CMDS:kick_add_maps.cmds.

OMIT_MAP

This macro randomly displaces all atoms, calculates structure factors so that it omits the "active" atoms from phasing and then returns coordinates to the original values and calculates an Fobs - Fcalc map.

The macro is "MAIN_CMDS:kick_omit_map.cmds".

KICK_MAP

This macro randomly displaces all atoms, calculates structure factors calculates an 2Fobs - Fcalc map and then returns coordinates to the original values

The macro is "MAIN_CMDS:kick_map.cmds".

MAIN Reference Manuals:KICKS File: kicks.txt
Last modified: 24-feb-2007

KICKS

KICK_0.3

Sets the maximal displacement of KICK for positions to default value 0.3A.

KICK_??

Defines the maximal displacement of KICK for positions. The values up to 1.0A are still treatable by the minimizer.

KICK_SEED

Sets the seed of the random numbr generator used for kicking to the specified number. After every kick command the seed increases by 1.

MAIN Reference Manuals:MAKE_DELETE File: make_delete.txt
Last modified: 27-sept-94

MAKE_DELETE

The MAKE_DELETE menu block is here to support your manual modeling of molecules either by allowing you to create or delete covalent BONDS (MAKE_BON, DELE_BON), manipulate the pair list (MAKE_PAIR, INIT_PAIR, PAIR_D_?) and on it based energy distance constrains (ENE_PAIR), create atoms in space (MAKE_ATO) and delete atoms included in the key 'active' (DELE_ACT).

MAKE_BON


> JOIN atom-num1  atom-num2

A covalent BOND between the last 2 PICKED atoms is formed.

MAKE_ATO


> make atom coordinate 3*real
> image color 222 select atom number natom end atom cross

MAKES an ATOM with the name X at the current image CENTER position and displays it as a CROSS.

MAKE_PAR


> make pair $2 $1
> define pair force force_pair pair dist 0.0 -
> select atom number #2 $1 end

MAKES a PAIR from the last 2 PICKED atoms and defines a distance constraint between them.

DELE_BON


> DELETE BOND atom-num1 atom-num2

A covalent BOND between the last 2 PICKED atoms can be DELETED or created (JOIN).

DELE_ACT


> delete atom select active end

DELETES current 'active' selection. You must confirm the deletion.

INIT_PAR


> make pair init

INITIALIZES the pair list by the setting pair counter to 0.

PAIR_D_?


> inquire PAIR_DIST "DISTANCE:"
> make pair atom-num1 atom-num2
> define pair force force_pair pair dist 0.0 -
> select atom number atom-num1 atom-num2 end

Asks for the target distance (PAIR_DIST) and MAKES a PAIR from the last 2 PICKED atoms and defines a distance constraint between them. MAIN Reference Manuals:MAP_CALC File: map_calc.txt
Last modified: 8-oct-2010

MAP_CALC

MAP_CALC menu block includes items performing map calculations.

It is loaded with the MAIN_CMDS:load_map_calc.com

For more information see also MAIN_DOC:calc_map/calc_map.html.

The only reason for leaving the items appart from the "CALC"MAP"is that the "create_map_calc.pl"accessible via Tk GUI does not cover the mluticrystal map calculations"calculations.

CALC_MAP

When using the right mouse button Tk GUI is invoked


 create_map_calc.pl
 -h|--help)        prints this message with available options and current status
 -m|--map)         map of [2FOFC+FOFC/2FOFC/FOFC/PHASE_COMB/FOBS/FCALC/3FO2FC] [2FOFC+FOFC]
 -o|--omit)        omit map [ON/OFF] [OFF]
 -b|--bulk)        bulk solvent correction [ON/OFF/USE] [ON]
 -a|--aniso)       anisotropic overall correction [ON/OFF/USE] [ON]
 -t|--target)      target function [UN/ML] current = [ML]
 -g|--generation)  map generation [FIRST/SECOND/THIRD] current = [FIRST]
 -y|--way)         map ways [SINGLE/KICK] current = [SINGLE]
 -k|--kick)        maximal xyz kick size [0.0 - 1.33]  current = [0.8]
 -r|--random)      kick size can be [FIXED/RANDOM/SERIES] = [FIXED]
 -c|--steps)       kick steps for averaging current = [30]
 -n|--number)      MAP number [1/2/3/4/5/6/7/8/9/10] [1]
 -s|--sharp)       B-factor sharpening for maps [ON/OFF] [OFF]
 -f|--sharp_fact)  B-factor sharpening factor [30]
 -p|--precision)   precision of density generation [1/2/3/4/5/6/7/8] [7]
 -w|--write)       write map files [ON/OFF] [OFF]
    --doit)        create the macro

help


        prints this message with available options and current status

map


         map of [2FOFC+FOFC/2FOFC/FOFC/PHASE_COMB/FOBS/FCALC/3FO2FC] [2FOFC+FOFC]

2FOFC+FOFC

Calculates both types of difference maps. Does not work with kick maps.

2FO-FC

Calculates an 2Fobs-Fcalc map from the last calculated structure factors using the MAIN_CMDS:calc_fofc_diff_map.cmds macro. It depends on the "ML_MAP" item. When on it used maximum likelyhood weighting and when off the least square weighting of resolution bins.

Subroutine arguments:

  • integer map number of a unit cell map (MAP_2FOFC)
  • real number multiplier of Fobs = 2.0
  • real number multiplier of Fcalc = 1.0

FO-FC_MAP

Calculates an Fobs-Fcalc map from the last calculated structure factors using the MAIN_CMDS:calc_fofc_diff_map.cmds macro. It depends on the "ML_MAP" item. When on it used maximum likelyhood weighting and when off the least square weighting of resolution bins.

Subroutine arguments:

  • integer map number of a unit cell map (MAP_FOFC)
  • real number multiplier of Fobs = 1.0
  • real number multiplier of Fcalc = 1.0

PHAS_CMB

MAIN calculates model structure factors via the "RE_PHASE" macro and writes them to a file, which is processed by a phase combination program invoked via a shell command. The resulting phases are then written to a file and read by MAIN, which then based on given FOBS, PHASES and WEIGHTS calculates a new FOBS map.

MAIN calls R. Read program SIGMA A, a program from CCP4, for phase combination procedure. The "create_phase_comb.pl" tool will create for you the necessary macros.

Subroutine arguments:

  • character variable or string of segment names used for structure factor calculations.
  • integer map number of a unit cell map (MAP_WORK) and

FOBS_MAP

Calculates an Fobs map on the basis of the read Fobs, corresponding phases and weights (figure of merit). You can use your own files.

omit

Calculates an "OMIT" map [ON/OFF]. When "ON" all key "active" atoms are excludedfrom structrue factor calculation.

bulk

Bulk solvent correction is "ON/OFF/USE" [ON]

Bulk solvent correction: toggles the flag ON or OFF. The actual optimization of linear and exponential coefficient is performed each time when structure factor calculation is performed.

See also MAIN_DOC:refine/refine.html.

aniso

Overall anisotropic correction: toggles the flag ON or OFF. The actual optimization of the 6 parameters defining the anisotropic distorsion is performed each time when structure factors are calculated.

See also MAIN_DOC:refine/refine.html.

target

Maximum likelyhood maps [ML] or uniform weight [UN] maps are calculated.

"ML" uses the "sigma A" formulation of maps weighting, whereas for "UN" the least square weighting is used. "ML" only works when the "TEST" reflection set has been defined.

See also MAIN_DOC:calc_map/calc_map.html.

generation

Calculates [FIRST/SECOND/THIRD] generations of maps - omitting the MAP nonconsistent atoms for the subsequent structrue factor calculation.

way

Map can be caluclated by two different ways [SINGLE/KICK]. "SINGLE" implies that the current set of atoms is being used, whereas for "KICK" maps a series of randomly displaced positions are being used.

kick

Maximal xyz kick size [0.0 - 1.33] current = [0.8]

series

Kick size can be [FIXED/RANDOM/SERIES] = [FIXED]

steps

Specifies the number of steps for KICK map averaging. default = [30]

number

Defines the MAP number [1/2/3/4/5/6/7/8/9/10] [1] in to which map will be loaded.

sharp

B-factor sharpening for maps [ON/OFF] [OFF]

sharp_fact

B-factor sharpening factor [30]

precision

Precision of density generation [1/2/3/4/5/6/7/8] [7]. The lower numbers may speed up calculations on the cost of accuarcy.

write

During map calculation each map generation can be stroed to a file for later use. write map files [ON/OFF] [OFF]

doit

Create the macro "generate_map.cmds"

KICK_0.3

Choose the displacement parameter ("KICK_0.3" or KICK_??"). For refinement 0.3 is maximum tolerated by the minimizer, whereas for kicked map much larger kicks (see"KICK_??") can be specified") can be specified.

KICK_??

Choose the displacement parameter ("KICK_0.3" or KICK_??"). For refinement 0.3 is maximum tolerated by the minimizer, whereas for kicked map much larger kicks can be specified"kicked map much larger kicks can be specified.

KICK_SEED

Sets the strating "SEED" for the random number generator. At each call, the seed variable "RAN_SEED" is increased for 1. The "RAN_SEED" is "MAIN" internal variable, which value can be directly set and inspected using the MAIN syntax:


> set  vari RAN_SEED
> show vari RAN_SEED

MAP_+_??

The number of maps generated by a different random number seed to average ("MAP_+_??"). The rule of a thumb is at least the kick parameter*10 repetitions.

KICK_MAP

For orientation:

  • At 3.A resolution kicks up and even beyond 0.8A are meaningful. At
    
     last 6 different maps should be averaged.
    
  • At 2.0A resolution kick up to 0.3 are reasonable. At last 3 different maps should be averaged.

With zero kick and averaging of 1 maps the resulting map is pure 2Fo-Fc map.

Averaged "2FO-FC" map is calculated by clicking "KICK_MAP".

Note that averaging "ML_MAP" maps occasionaly result in maps worse that the "ML_MAP" without kicking.

OMIT_MAP

An averaged omit map is calculated by clicking "OMIT_MAP". With zero kick and averaging of one maps the resulting map is pure Fo-Fc map. The parts selected in the current key "active" are omitted from structure factor calculation. Apply the same kicks and numbers of maps for averaging as for the kick maps.

MAIN Reference Manuals:MAPS_EDIT File: maps_edit.txt
Last modified: 29-sept-94

MAPS_EDIT

MAPS_EDIT together with the MAPS_IMAGE blocks enable you to interactively create and modify electron density maps under visual control. (MAP_ACT? items of both blocks are identical

  • they both reffer to the same variable.)

Essential oparations as map creations (MAP_NEW) to initial values (MAP_CLEA, MAP_MASK) can be performed.

Map values can be set directly (MAP_SET?), copied from another map (MAP_COPY) scaled (MAP_SC.?) or rescaled (MAP_RESC).

Two maps can be merged (MAP_MR.?) and added (MAP_ADD) together. Cavities within masks can be filled (MAP_FIL?) and a unit cell density can be generated (MAP_CELL).

Some previous knowledge of the MAKE MAP command syntax is recommended.

MAP_PAS?

MAP_ACT?

MAP_NEW


> make map map_to from map_from initial map_val number

MAP_AROU


> menu block MAPS_EDIT item MAP_AROU add \
> text "<MAIN_CMDS:make_map_around.cmds"

The '>MAIN_CMDS:make_map_around.cmds' file has the following syntax:


> inquire ato_grid "GRIDS AROUND ATOM BOX:"
> make map map_to from map_from init map_val number -
> around ato_grid select active end
> return

MAP_CLEA


> menu block MAPS_EDIT item MAP_CLEA add text -
>  "set variable map_val = -9999"

MAP_MASK


> menu block MAPS_EDIT item MAP_MASK add text -
>  "set variable map_val = 9999"

MAP_SET?


> menu block MAPS_EDIT item MAP_SET? add text "<MAIN_CMDS:make_map_set.cmds"

MAP_COPY


> menu block MAPS_EDIT item MAP_COPY add text -
>  "make map map_to from map_from copy"

MAP_SC.?


> menu block MAPS_EDIT item MAP_SC.? add text "<MAIN_CMDS:make_map_scale.cmds"

MAP_RESC


> menu block MAPS_EDIT item MAP_RESC add text -
>  "make map map_to from  map_from rescale"

MAP_MR.?


> menu block MAPS_EDIT item MAP_MR.? add text "<MAIN_CMDS:make_map_merge.cmds"

MAP_ADD


> menu block MAPS_EDIT item MAP_ADD  add text -
>  "make map map_to from map_from add"

MAP_FIL?


> menu block MAPS_EDIT item MAP_FIL? add text "<MAIN_CMDS:make_map_fill.cmds"

MAP_CELL


> menu block MAPS_EDIT item MAP_CELL add text -
>  "make map map_to from map_from cell"





MAIN Reference Manuals:MAP_MASK


MAP_MASK

Menu itesm in "MAP_MASK" help you to recognize and select the asymmetric unit for either further density modifications (solvent falttening and averaging) or model building.

The menu block "MAP_MASK" is loaded with macro "MAIN_CMDS"load_map_mask.com"to page No. 10"to page No. 10.

SCOR_MAP

This is a pre-step for density modification procedures. Creates score map which serves as the basis for differentiation of solvent and macromolecule regions.

The analysis shows (SHOW ANAL) which density score level approximately separates molecular from solvent region. You are advised to display the score map and carefully inspect it at different contouring levels and then decide about your solvent content and cutoffs.

The macro MAIN_CMDS:map_mask_score_map.cmds is only an example that should be adjusted to almost each particular case. The procedure calls MAIN_UTILS:solvent_mask_solomon.com, which you may also wish to edit.

SKEL_GEN

Skeletonizes a map. The macro finds extrems and connects them through saddle points. Extreme and saddle points are converted to atoms and connections to covalent bonds between them.

It is assumed that the MAP_2FOFC, or MAP_FO (both variables) point to the map number 1, which is by default a unit cell map that will be skeletonized. In order to change the box in which skeletonization is performed copy the MAIN_CMDS:map_mask_skel_gen.cmds macro to your working directory and tailor it to your needs.

If it happens that you run out of memory limits, choose a larger MAIN version or skeletonize only a portion of a map.

See also the chapter "Molecular replacement" (MAIN:doc/mol_repl/mol_repl.html).

SKEL_IMA

Displays image of "skeleton" atoms in two colors. The skeleton atoms selected in the key "active" are shown in different color.

The default macro is MAIN_CMDS:map_mask_skel_ima.cmds.

SKEL_SYM

Displays image of the symmetry equivalents of the "active" skeleton atoms. Used to verify overlap of the "active" atoms with its surroundings during a search for asymetric unit.

The default macro is "< ?MAIN_CMDS:map_mask_skel_sym.cmds". MAIN Reference Manuals:MINIMIZE File: minimize.txt
Last modified: 28-sept-1994

MINIMIZE

Atoms SELECTED in KEY "active" are MINIMIZED against background of "passive" KEY atoms with the ENERGY terms turned ON. 'active' atoms are allowed to move and 'passive' atoms are there only to interact with 'active' atoms. The key 'passive' should include all 'active' atoms, otherwise 'active' atoms will not be treated properly.

When applying PAIR constraints take care that anchor do not become a part of the 'active' key. Anchors do not need to be included to the 'passive' key.

MINI_ANH minimizes anchors in an electron density map gradients. I recommand you to use this option a lot.

See for example the >utils/def_top_par_19.com file, which is the default macro invoked through the "DEFINE" item. You can redirect these calls by redifining the variable DEF_ALL. Try


> show vari DEF_ALL

to check the variable status.


> defin clas charge by topo
> defin bond angle by auto
> defin dihe improper by topo

DENSITY energy term is a negative correlation of a "real" atom with the density of the chosen map. For comfort model building see also the below session "Use of anchors" and the session "Load_xray_maps" in the part "Dialog mode accessories".


> ener density map 1 density scale 30.

MAIN Reference Manuals:MODELER File:>doc/menu/modeler.txt
Last modified: 27-sept-2002

MODELER

The modeling functions ("MOV_SELE", "RT_CHAIN", "RT_BETWEE", "MOV_ATOM", "MOV_RESI", "TRANSLATE", "MOV_DIST", "MOV_RT_6", "RT_ANGLE") activate OBJECTS for interactive spatial modifications of molecular geometry and assign DIALS to them. After the geometry has been changed using mouse or dials, the change has to be accepted using "OBJ_ACCE" or rejected "OBJ_REJE".

Remember first to pick the atoms and afterwards pick an ITEM. The last picked atoms may be used any number of times.

All these commands can be applied in any combination on various or the same group of atoms. The order in which they are applied does matter - eroneous combinations may result in eroneous results (first defien bodn rotation and the a rigid body bovement of the moving atoms by "MOV_RESI" or "MOV_SELE".

(See also DIAL_SAV and DIAL_RST regarding DIAL set storage end retrivial.)

The "INV_CHIR" and "CONNECT" act instantaneously and do not need any DIAL action or aproval ("OB_ACCEPT").

See also MAIN_MENU:history.html and MAIN_MENU:nice_sel.html.

MOV_SELE

Does rigid body movement (combines "ROTATION" and "TRANSLATION") of the selected atoms (key "active") using the last PICKED atom as the center of rotation. The simplest way of selecting atoms is using the functions of the menu block nice_sel.html. Shortcut is "x.

MOV_RESI

Does rigid body movement (ROTATES and TRANSLATES) of the residue disregarding the connectivities of that particular residue. (You don't have to break bonds as in the case of the "ROT_TRAN" command.) The center of rotation is the last picked atom.

ROTATE

ROTATE the molecule of the last PICKED atom. Useful if you do not want to move a molecule but only adjust its orientation.

TRANSLATE

TRANSLATES the molecule of the last PICKED atom. Useful if you do not want to change orientation of a molecule but only adjust its position

MOV_ATOM

TRANSLATES the last PICKED atom disregarding its connectivities. (You don't have to break bonds as in the case of the TRANSLAT command.)

Does not save the DIAL set automatically.

RT_CHAIN

RT_CHAIN activates rotation of all BONDS between the last 2 PICKED atoms. MAIN is only capable of checking each separate bond rotation. When there are more bonds to be rotated in the chain and one is a part of a ring, an error message will appear. In such case you should hit "OB_REJECT" and pick a different pair of atoms.

The menu item "RT_CHAIN" calls within a loop a variety of command files, one for each rotatable bond. After each 8th bond, the DIAL WRITE sentence is automatically done.

RT_BETWE

Rotate all atoms, which are part of covalent bond network, between the last two picked atoms. The command was created to enable adjustments of a peptide bond orientation by clicking on two neighboring CA atoms and then activation the function.

RT_ANGLE

Takes the last 3 atoms from the HISTORY list ($3, $2, $1) and modifies angle between them. Atoms on the $2 atom side of the bond ($3 - $2) are rotated about the axis perpendicular to the plane defined by the last three atoms and going through the atom $2.

MOV_DIST

Moves (translates) the molecule of the last PICKED atom in the direction of the vector connecting the last two PICKED atoms. When the atoms are connected via a covalent bond, then on the atoms on the side $2 (first picked) atom is moved.

MOV_RT_6

Activates 3 BOND and 2 ANGLE rotations and 1 DISTANCE movement. This is an INTERNAL (relative) coordinate way of ROTATION and TRANSLATION (ROT_TRAN) function that is applied in absolute (cartesian) coordinate space. The last 6 PICKED history atoms are required.

This is an internal coordinate alternative to ROT_TRAN function. It also includes 6 degrees of freedom.

Automatically saves the DIAL set.

INV_CHIR

Interchanges the positions of the two side chains attached to a single atom. In other words: inverts the chirality of the common neighbour of the last 2 PICKED atoms.

CONNECT

Moves the first picked molecule into a reasonable binding geometry against to the second picked molecule and forms a covalent bond between the last two picked atoms. You may wish to rotate about the newly formed bond to improve its' dihedral conformation (see "RT_CHAIN").

Acive objects

OB_START


> OBJECT int SET INIT

OB_REJEC


> OBJECT int SET TRUE

OB_ACCEP


> OBJECT int SET FALSE

These commands affect all activated OBJECTS. The objects are either returned to their initial position ("OB_START"), rejected (OB_REJEC) or accepted ("OB_ACCEP"). Only "OB_ACCEPT" changes atom coordinates. After "OB_REJEC" and "OB_ACCEP" the complete image is redrawn. MAIN User`s guide:Mouse usage File: MOUSE.TXT

Mouse usage

Last Modified: 27-sept-94

When the cursor is in the IMAGE window, the mouse can be used beside for picking atoms as a substitute input from dials. (The dials substitution is disabled on the ESV computers.) The mouse has 3 buttons: left (L), middle (M) and right(R). When one or two of them are pressed and moved, they replace input from the current dials set. By default:

The left button (L) can control rotations around X, Y and Z axis. When the cursor is moved within a circle of the image window center, the horizontal movements correspond to rotation about Y axis and vertical about X axis. If cursor is moved outside the circle, its' movement results in rotation about Z axis.

The middle button (M) controls translations along X and Y direction.

The left and middle button (LM) pressed together and moved vertically; they translate image along the Z direction.

The right button (R) controls scaling of the image (zoom). When cursor is moved towards the center of the image window, the image is shrunk, and when it is moving away from it, the image is expanded.

The right and middle button (RM) pressed together control clipping. When the cursor is moved towards the center of the image window, the clipping planes are moved together, and when it is moving away from it, the separation between the clipping planes is increased.

Changing dial definitions will also change the mouse button functions. In general, pressed middle button (M) mimics dials 1 and 2, pressed left and middle button (LM) mimic dial 3, right button (R) mimic dial 4, left button (L) mimics dials 5, 6 and 7, and combination of right and middle button (RM) mimic dial 8.

Releasing a mouse button while still moving the cursor results in a continuation repetition of the last move before the release. So smooth rotations of image on the screen can be achieved.

Mouse trouble shooting

When mouse doesn't behave properly it needs to be resetted. This happens quite often (on HP it is a rule) when the image window is iconized and then restored.

So reset the mouse by pressing any keyboard character key or type commands


> image mouse off
> image mouse on

If you get anoyed with dial rotations (you are unable to pick atoms because you keep moving the image), turn the mouse dial mimicking functions off:


> image mouse off

MAIN Reference Manuals:NICE_SEL File: nice_sel.txt
Last modified: 24-feb-2007

NICE_SEL

NICE_SEL is quick summary of more useful and ruther extensive SELECT menu block and SELECT commands. The most commonly used combinations of the SELECT menu have been merged into a single click.

Clicking the items manuipilates the selection keys "active" and "passive" thus primarily supporting energy calculations.

The NICE_SEL menu is loaded with the file MAIN_CMDS:load_nice_sel.com.

ADD_MODE

Add mode describes weather the newly selected atoms (using the menu items belowe ) will be added to the currently selected "active" and "passive" ones or will they replace the current selection. By default ADD_MODE is off (indicated by empty button).

The "ADD_MODE" calls the macros MAIN_CMDS:sel_add_mode_on.cmds and MAIN_CMDS:sel_add_mode_off.cmds. The call is mode dependent.

ACT_WORK

ACT_WORK selects in the "active" the atoms of the "WORK_SEGM" list of segmnet IDs.

ACT_SGID

ACT_SGID selects in the "active" the atoms of segment IDs equal to the last clicked atom.

ACT_SEGM

ACT_SEGM selects in the KEY "active" the atoms attached to the last picked atom through a network of covalent bonds, the KEY "passive" includes all "active" atoms.

ACT_2RES

ACT_2RES selects in the KEY "active" all atoms between the last two picked atoms. The KEY "passive" includes whole residues of all "active" atoms plus all covalently attached residues.

The "ACT_2RES" calls macro MAIN_CMDS:sel_active_2res_rang.cmds.

ACT_NEIG

ACT_NEIG selects in the KEY "active" all atoms that are a certain number of steps through covalent bond network away from the last clicked atom.

The "ACT_NEIG" calls macro MAIN_CMDS:sel_active_neigh.cmds.

ACT_LAST

ACT_LAST selects in the KEY "active" all atoms of the last clicked residue. from the last clicked atom.

FIX_ATOMS

FIX_ATOMS removes all clicked atoms from the key "active". Thereby these atoms are fixed at their positions during following minimization runs.

The "FIX_ATOMS" calls macro MAIN_CMDS:sel_fix_atoms.cmds.

ANCHOR

ANCHOR introduces anchors to each picked atom. Atoms are pulled against their anchors with a harmonic force. ANCHORS are freealy movable adn can be minimized against an electron density map (MINI_ANC).

The "ANCHOR" calls macro MAIN_CMDS:sel_anchor.cmds.

MAIN Reference Manuals:N_MOLECUL File: nmol.txt
Last modified: 22-jul-2002

N_MOLECUL

Items of the menu block "N_MOLECUL" assist in model building ("WORK", "PUT_TO", "GET_FROM","GOTO_SEQ", CRE_OTHE") in the cases, when there is more than one equal molecule in an asymmetric unit of one or several crystal forms. The segment ID items ("SID_????") submit the segment name as argument to the"WORK","PUT_TO"."GET_FROM"and"GOTO_SEQ" modes. There are as manu"SID_"items as there are segment IDs"items as there are segment IDs.

The working modes ("WORK", "PUT_TO", "GET_FROM") are set via MAIN_CMDS:nmol_work_mode.cmds, wheras the segment ID items ("SID_????") invoke MAIN_CMDS:nmol_action.cmds macro.

The menu is created with "main_config" tools command (MAIN_CONF:create_load_nmol.pl) and loaded by running a "read.com", wheras the other macros are generated in "dens_mod" section ("MAIN_CONF:menu_dens_mod.sh") or parts even at run time. For example of a load file see MAIN_DOC:nmol/load_4mol.com.

For a more general frame of appliactions see MAIN_DOC:nmol/nmol.html

WORK

Sets the mode to "WORK", meaning that the next clicked "SID_????" will trigger a new definition of a working segment and display images of all equivalent molecules superimposed to the working segment.

PUT_TO

Sets the mode to "PUT_TO", meaning that the next clicked "SID_????" will copy conformation and occupancy of the "active" key atoms from the currently working segment to the equivalent part of the designated molecule.

"PUT_TO" is on opposite of "GET_FROM".

GET_FROM

Sets the mode to GET_FROM, meaning that the next clicked SID_???? will copy conformation and occupancy of the equivalent part of the SID_???? to the working segment "active" key atoms.

"GET_FROM" is on opposite of "PUT_TO".

GOTO_SEQ

Sets the mode to GOTO_SEW, meaning that the next clicked SID_???? will move the center of the 3D image to the center of the residue with the same sequence ID on SID_???? as has last been clicked (picked to history list).

CRE_OTHER

Creates all equivalent molecular segments in the group from the current working segment using the local symmetry operators from the file.

ROT_MAPS

Will rotate maps of equivalent segments to the current working segment mask. The macro is created when the "WORK" segment is chosen. MAIN User`s guide:Origin of the name Depp Pages

Origin of the name Depp Pages

"Depp pages" stand for "moron pages". "Depp" in German is an equivalent of "moron". The name is an original contribution from Robert Huber, who in the early days of program development has said that he would use the program, if it had menus for a "depp" like himself.

MAIN Reference Manuals:REFINE File: refine.txt
Last modified: 8-oct-2010

REFINE

  • NCS
  • CRYST_NCS
  • FLAT_B25
  • KICK_B_5
  • REF_B
  • REF_OCCU
  • GEN_SOLVENT

    Controls interactive positional, B-value, and occupancy refinement of "WORK_SEGM" atoms. By clicking the right mouse button Tk GUI is used to invoke the configuration menus.

    KICK_XYZ

    KICK_XYZ displaces all "WORK_SEGM" atoms up to the current "KICK_VAL" shift.

    REF_XYZ

  • NCS
  • CRYST_NCS

    
      create_refine.pl
     -h|--help)      prints this message with available options and current status
     -s|--step)      sets number of minimization steps per cycle [300]
     -k|--kick)      sets starting and final maximal xyz kick [0.0 - 0.33]
                     current = [0.3 - 0.2]
     -c|--cool)      sets number of cooling cycles  [0]
     -b|--bramp)     sets minimal and maximal starting atomic B-value ramp [5 - 60]
     -t|--target)    target function for refinement [MAP/LSQ/ML/REAL_SPACE/REFMAC]
                     current = [ML]
     -r|--ratio)     approximate ratio target for bond deviations  [0.005 - 0.1]
                     current = [0.02]
     -m|--map)       MAP for DENSITY refinement [1]
     -w|--way)       way of reciprocal space refinement [ACCURATE/FAST] [FAST]
     -n|--ncs)       Non-Cryst-Similarity NCS energy flag [ON/OFF]
                     current = [OFF]
     -g|--gncs)      Non-Cryst-Similarity NCS geometry force = [5]
     -y|--cryst_ncs) Refine in variety of crystal forms [ON/OFF]: current = [OFF]
     -x|--backup)    backup after each cycle [ON/OFF]: current = [OFF]
     -f|--free)      r-free flag [ON/OFF] current [ON]
     -o|--output)    set file name of the created macro [refine.cmds]
        --doit)      create the macro
    

    Refines positions of your model using macro "refine.cmds".

    Positional refinement

    The simplest way to configure is to click on the "REF__XYZ" on the "REFINE" depp page using the right mouse button. A configuration GUI will show up.

    Alternatively you can configure it via the command line interface by running the MAIN_CONF:create_refine.pl script by yourself.

    MAIN_CONF:create_refine_b.pl) to create and adjust your local "refine.cmds" macro and "refine_b.cmds" as it defines groups and forces for non-crystallographic similarity constraints as well.

    After the "refine.cmds" has been configured click "REFINE" and run it.

    Configure "refine.cmds"

    
    > create_refine.pl
    
    -h|--help) prints this message with available options and current status -s|--step) sets number of minimization steps per cycle [300] -k|--kick) sets starting and final maximal xyz kick [0.0 - 0.33]
    
                    current = [0 - 0]
    
    -c|--cool) sets number of cooling cycles [0] -b|--bramp) sets minimal and maximal starting atomic B-value ramp [5 - 100]

    -t|--target) target function for refinement [MAP/DIFF/LSQ/ML/ML_EST/ML_APR]

    
                    current = [ML]
    
    -a|--atoms) missing atoms for estimation of ML [100] -r|--ratio) approximate ratio target for bond deviations [0.005 - 0.1]
    
                    current = [0.01]
    
    -m|--map) MAP for DENSITY refinement [1] -x|--xmap) MAP for X-DIFF refinement [3] -q|--qmap) MAP for rec. space refinement [3]

    -n|--ncs) Non-Cryst-Similarity NCS energy flag [ON/OFF]

    
                    current = [ON]
    
    -g|--gncs) Non-Cryst-Similarity NCS geometry force = [5] -y|--cryst_ncs) Refine in variety of crystal forms [ON/OFF]: current = [OFF]

    -o|--output) set file name of the created macro [refine.cmds]

    
       --doit)      create the macro
    

    The "MAP/DIFF/LSQ/ML/ML_EST/ML_APR" are target functions "-t|--target" that can be used in refinement. The "ML_EST" requires also an estimate of missing number of atoms "-a|--atoms". Pavel Afinine said that 25% error in estimate is still good enough.

    Maps used in refinement are defined by "-m|--map", "-x|--xmap", "-q|--qmap", whereas the strength of the target terms is controlled via the ratio between traget and chemistry terms. Geometry violations printed out during each step of refinemeny will tell you if your RATIO is too low or too high. (See also ANA_BOND and ANA_ANGL in MAIN_MENU:analysis.html).

    Before refinement it makes sense to "KICK_ALL" the atomic coordinates to jump out of the current state (heat the atoms to several 1000 K) and then let the minimizer cool down the molecule in the "fast cooling" procedure. Multiple kicks "-k|--kick" can be applied in a number of cooling cycles "-c|--cool", each cycle with the maximal along the line of the two specified kick values.

    Refinement output writes the "step" number, "stepsize", total energy "summ", average "gradient" and values for each particular energy term turned on. "Density" is the map constraint term, whereas "r-value" is only listed, its value changes only when structure factors are recalculated.

    Note that refinement using NCS across several crystal forms is possible too.

    
     step:     15      stepsize: 0.63802867E-13
     summ:    -6507.4916 grad:       24.2193 bond:      169.3255 angl:      663.3933
     dihe:     1206.1670 impr:      135.8787 vdw :     -236.2183 elec:    -4877.6440
     dens:    -3568.3938 rval:       37.0655
    

    Applying NCS constraints

    Non-Crystallographic-Symilarity Constraints can be applied between equivalent molecular parts of in principle unlimited number of equivalent regions within a single crystal as well as among several crystal forms.

    NCS

    When approaching the end of structure determination you are advised to edit the file "define_key_out.com" in order to remove the non-super imposable residues from the NCS constrains forces.

    
     key out sele .not all end
    < define_key_out.com
    

    The "define_key_out.com" macro would look something like this:

    
     key out sele ( seq  x1 x4 y16 : y27 ) \
             end
    

    The lines below show how it is possible to impose stronger NCS constraints on main chain atoms (FORCE 20.) and slightly weaker on the side chain atoms (FORCE 5.) An example MAIN_DOC:nmol/refine.cmds file is in the MAIN_DOC:nmol/ directory.

    
     define init constrain ncs
     define constraint ncs \
        sele ( segm name MOLA .a .not out ) .a atom name CA N C O H end
     define constraint ncs
        sele ( segm name MOLB .a .not out ) .a atom name CA N C O H end
     define constraint ncs force 20.
     define constraint ncs b-force 0.04
    

    
     define constraint ncs next
     define constraint ncs \
                 sele segm name MOLC .a .not atom name CA N C O H end
     define constraint ncs \
                 sele segm name MOLD .a .not atom name CA N C O H end
     define constraint ncs force 5.
     define constraint ncs b-force 0.01
    

    It does make sense to verify the success of the NCS groups creation. Since equivalent atoms are the consecutive ones in the both selections the NCS keys should contain at least the same number of atoms:

    
     show key
    

    
    SHOW> KEY:   9 int_ncs__1 SELECTED  254 OF TOTAL 6176
    SHOW> KEY:  10 int_ncs__2 SELECTED  254 OF TOTAL 6176
    

    The next more sever test (good for debugging) is to create PAIR lists and see, whether the equivalent atoms match by their atomic, residue and sequence names or not.

    
     make pair init select int_ncs__1 end select int_ncs__2 end
     write pair
    

    If you want to be sure the default initial guess will work well calculate the superposition parameters before the minimizer starts to work:

    
     define constraint ncs auto_guess
    

    
    RMS_FIT> PARAMETERS X-ROT: 191.373 Y-ROT": 111.292 X-ROT"":  35.276
    XYZ-TRAN:  88.258   6.726  15.660 RMS-FIT   .452"XYZ-TRAN:  88.258   6.726  15.660 RMS-FIT   .4520
    

    The "RMS-FIT" value should look reasonable. Values above 3. are very likely to mean that the selections are not properly defined and maybe that the procedure did not converge properly.

    Instead of leaving all 6 degrees of freedom (3 rotation axis and translation component) one can also fix some of the parameters (with flag exual 0), by providing initial guess and fixing the rotational axis (in thes case the 2-fold). Use of the matrix defined by polar angles is certainly the choice here:

    
     rms coor all eigen \
      sele segm name MOLB end sele segm name MOLA end
    

    
     show rms
    

    
     defin constr ncs polar \
           set_gues 2 RESULT_0 RESULT_1 180.0 RESULT_3 RESULT_4 RESULT_5 \
           flags 1 1 0 1 1 1
    

    The energy term is turn on with the NCS ON command

    
     energy ncs on
    

    CRYST_NCS

    When refining a molecular model in two or more crystal forms means that each model should interact with its own diffraction data and own unit cell. Converted to MAIN language it means, that each molecule should interact with its own crystal form difference Fourier map during a refinement procedure and that all energy interactions between the molecular models, besides the NCS term, should be excluded.

    The setup is done through the MAIN_CONF:create_main_config.pl , where segment IDs bind structrue to tehir crystal forms, which require cell constants file, space groups and diffraction data specified via theMAIN_CONF:create_read.pl.

    From a user perspective, apart from the above mentioned additional specifications, the case is not much different from the case with several molecules in one crystal form.

    OF course the cros "crystal" term should be on.

    FLAT_B25

    Flattens B-values of all "WORK_SEGM" atoms to 25.

    KICK_B_5

    Kicks B-values of all "WORK_SEGM" atoms with the maximum kick of 5.

    REF_B

    
     create_refine_b.pl
      -h|--help)    prints this message with available options and current status
    -v|--over)    overall B-value refinement  steps [-1 off;>0 on] = [-1]
    -s|--step)    ind. B-value refinement  steps [-1 off;>0 on ] = [20]
    

    
      -k|--kick)    sets starting and final maximal B-kick [0 - 30] current = [0 - 0]
      -c|--cool)    sets number of cooling cycles = [0]
    

    
      -d|--define)  define group organisation [SINGLE/ATOM/RESIDUE/SEGMENT] = [SINGLE]
    -p|--bond)    B-value bond inter-group constrain force [-1.0 off;> 0.0 on] = [1.4]
    -g|--group)   B-value intra-group constrain force [-1.0 hard;> 0.0 soft] = [-1]
      -b|--bramp)   bramp interval of valid B-values = [5 - 60]
    

    
      -w|--way)     way of reciprocal space refinement [ACCURATE/FAST] [FAST]
      -t|--target)  target function for refinement [LSQ/ML]
                    current [ML]
      -r|--ratio)   approximate ratio target for standard deviations of boned B-values [1. - 10.]
                    current = [2]
      -n|--ncs)     Non-Cryst-Similarity NCS B-value flag [ON/OFF] = [OFF]
      -f|--fncs)    B-value NCS force  = [0.004]
    

    
      -o|--output)  set file name of the created macro [refine_b.cmds]
         --doit)    create the macro
    

    Refines B-values of a model (individual and overall) against the chosen target function using macro "refine_b.cmds". Refines positions of your model using macro "refine_b.cmds".

    After the "refine_b.cmds" has been configured click "REF_B" to run it.

    For B-value refinements only four "LSQ/ML/ML_EST/ML_APR" out of six target functions "-t|--target" can be used. "MAP" and "DIFF" make no sense. The "ML_EST" requires also an estimate of missing number of atoms "-a|--atoms". Pavel Afinine said that 25% error in estimate is still good enough.

    Before refinement atomic B-factors can be kicked. Similarly as in positional refinement, consecutive kicks can be applied in cycles.

    Overall B-value refinement

    Overall B-value refinement is based on Wilson plot statistics comparing Fobs and Fcalc in separate shells.

    
    > mini b-val overall sele segm name SEGMENTS end step 3
    

    Individual B-value refinement

    For B-value optimizations GROUPS have to be DEFINED. The group definitions are located at the top of a MAIN_CMDS:refine_b.cmds macro.

    The smallest group is an atom and the largest are all atoms. Between these two extremes any number of groups composed from any combination of atoms is valid. Currently GROUPS can be defined through SINGLE, ATOM, RESIDUE and SEGMENT command words. The GROUP SINGLE command defines single atoms group - each selected atom is a separate group. The GROUP ATOM defines all selected atoms as a group. The GROUP RESIDUE command DEFINES each selected residue as a group and the GROUP SEGMENT does the same on the segment level.

    
    > define init group
    > define group atom select all end
    > define group single select all end
    

    The MINIMAL and MAXIMAL atomic B-value specify in which limits can B-factors of individual atoms be optimized. Once defined, they serve as a contraints to return the "escaped" B-values into the defined limits.

    Oppose to the measured data, which try to scatter atomic B-values, several restraining terms try to make neighboring atomic B-values similar to each other. The ANGLE, BOND, GROUP force constants pull together B-values of groups that are linked by covalent BONDS or ANGLES. The smallest group (by default) is an individual atom. A GROUP restraint is hard when the GROUP force is set to a negative value. Otherwise atoms are pulled towards the arithmetic middle of each group. Negative BOND and ANGLE force constants turns these restrains off.

    
    > ener minimal = 5.0 \
    > maximal = 80. \
    > b-val bond = 1.444 \
    > b-val angle = 1.0 \
    > b-val group = -1.0
    

    Similarly as in position refinement, in B-valu refinement, the BOND RMS deviations serve as the aim to derive the scaling constant.

    
    > mini b-val 2.0
    

    is the default.

    Besides, non-crystallographic-similarity, NCS, constraints can be applied. These constraints refer to the same groups which are used in positional refinement. See MAIN_DOC:nmol/refine.cmds. The NCS B-FORCE constant pulls the B-values of similar atoms towards their arithmetic middle.

    
    > define constr ncs b-force 0.1
    

    Before start of minimization B-values of selected atoms can be kicked in order to shift refinement from the current (local minimum) position.

    
    > set temp kick = 4. sele segm name SEGMENTS .and. weight 0.1 1.1 end
    

    B-value for refinement with an ENERGY command and then start MINIMIZATION. Command below submits 10 cycles of B-VALUE refinement. Energies will be WRITTEN each iteration step.

    
    > mini b-val indiv  sele segm name SEGMENTS end step 10 writ 1
    

    An equilibrated assignment of B-VALUE scales is essential for a succesfull refinement. Values as BOND 1.0 for example result in an equal B-value for all atoms. After refining a structure check the B-VALUES sigmas with a SHOW TEMPERATURE command, and if necessary increase or release the force of constraining terms.

    See also to the MAIN_DOC:1mol/1mol.html example.

    Subroutine arguments:

    • integer map number of a unit cell map (MAP_WORK) and
    • character variable or string(s) of segment names used for structure factor calculations.

    For more see MAIN_DOC:refine/refine.html.

    REF_OCCU

    
     create_refine_b.pl
      -h|--help)    prints this message with available options and current status
    -v|--over)    overall B-value refinement  steps [-1 off;>0 on] = [-1]
    -s|--step)    ind. B-value refinement  steps [-1 off;>0 on ] = [20]
    

    
      -k|--kick)    sets starting and final maximal B-kick [0 - 30] current = [0 - 0]
      -c|--cool)    sets number of cooling cycles = [0]
    

    
      -d|--define)  define group organisation [SINGLE/ATOM/RESIDUE/SEGMENT] = [SINGLE]
    -p|--bond)    B-value bond inter-group constrain force [-1.0 off;> 0.0 on] = [1.4]
    -g|--group)   B-value intra-group constrain force [-1.0 hard;> 0.0 soft] = [-1]
      -b|--bramp)   bramp interval of valid B-values = [5 - 60]
    

    
      -w|--way)     way of reciprocal space refinement [ACCURATE/FAST] [FAST]
      -t|--target)  target function for refinement [LSQ/ML]
                    current [ML]
      -r|--ratio)   approximate ratio target for standard deviations of boned B-values [1. - 10.]
                    current = [2]
      -n|--ncs)     Non-Cryst-Similarity NCS B-value flag [ON/OFF] = [OFF]
      -f|--fncs)    B-value NCS force  = [0.004]
    

    
      -o|--output)  set file name of the created macro [refine_b.cmds]
         --doit)    create the macro
    
    dus@zap $ create_refine_occ.pl
    
      -h|--help)    prints this message with available options and current status
    -s|--step)    ind. B-value refinement  steps [-1 off;>0 on ] = [20]
    

    
      -t|--target)  target function for refinement [LSQ/ML]
                    current [ML]
      -o|--output)  set file name of the created macro [refine_occ.cmds]
         --doit)    create the macro
    

    GEN_SOLVENT

    
     create_gen_solv.pl
      -h|--help)      prints this message with available options and current status
      -b|--b_value)   B-value cut for previous rounds in WAT [70.0]
      -p|--peak)      peak threshold in diff density map (fo-fc) [2.3]
      -d|--density)   density map (2fo-fc) cutoff [1.1]
      -c|--close)     the closest density pick existing atom distance [2.3]
      -e|--empty)     the distance to the closest empty occupancy atom [4.5]
      -f|--far)       the farthest density pick distance to an existing atom [4.5]
      -m|--merge)     remove symmetry related peaks if they get closer than [2.3]
    -l|--list)      key "check_list" contains residues closer than [2.5] to peaks
    -i|--ion)       key "ion_list" conatins WAT atoms with fo-fc dens higher than [2.0]
      -w|--what)      what to do: [CHECK/NEW/BOTH] [BOTH]
         --doit)      create the macro
    

    Generates new solvent molecules on the basis of peaks in a difference density map, checks their consistency within an 2Fo-Fc map, their distance to hydrogen bond donors and overlap with already existing atoms and symmetry overlap.

    The newly created solvent molecule (H2O) obtain segment name WAT2. HINT: Modify your RE_IMAGE command to see the newly created solvents in a different color.

    The macro invoked by default is the file MAIN_CMDS:gen_solvent.cmds, which calls MAIN_UTILS:gen_solvent.com, created by "menu_gen_solv.sh" script.

    Subroutine "gen_solvent.com" arguments:

    • integer map number of a 2fo-fc unit cell map (MAP_2FOFC),
    • integer map number of a fo-fc unit cell map (MAP_FOFC),
    • character variable or string(s) of segment names around which new solvents will be added,
    • character variable or string(s) of segment names around which new solvents will be added, which do not include any solvent molecule in order to enable control of solvent layers added.

    MAIN Reference Manuals:RENAME File: rename.txt
    Last modified: 20-Oct-97

    RENAME

    RENAME menu is a set of commands that allow you to RENAME atom, resiude, sequence and segment names.

    The menu block RENAME is loaded with the command '<>cmds/load_rename'.

    THE ACT_SEGM and ACT_2RES are two the most often rewuired combinations otherwise accessible through the SELECT menu.

    REN_ATOM

    RENAMES ATOM NAME of the last picked atom. You are prompted for a string!

    REN_RESI

    RENAMES RESIDUE NAME of the last picked residue. You are prompted for a string!

    REN_SEQ

    RENAMES SEQUENCE ID of the last picked residue. You are prompted for a string! Take care: The new sequence name must be typed within double quotes, for example as "125" to force MAIN to interpret 125 as a string and not as an integer!!! (A very common source of problems.)

    AUTO_SEQ

    RENAMES SEQUENCE IDs of the key 'active' selection. You are prompted for a sequence root.

    REN_SEGM

    RENAMES the SEGMENT NAME of the segment to which the last clicked atom belongs to. You are prompted for a string!

    MAIN Reference Manuals:RMS_FIT File: rms_fit.txt
    Last modified: 18-nov-97

    RMS_FIT

    The RMS_FIT items superimpose two molecules using a RMS fit procedure. They rotate and translate the "from" segments "to" the target segments.

    The RMS_FIT menu block is loaded with the file MAIN_CMDS:load_rms_fit.com. If you want more than provided then copy the macro MAIN_UTILS:rms_fit_1_to_2.com to your working directory and modify it.

    FIT_PAIR

    If molecules are far from being superimposed and you can not use the "FIT_SEQU" item, because sequence id's are not related as well provide your pair list manually. Go to page 1 and click INIT_PAR to initialize the pair list and then after picking each pair off atoms you want to superimpose click MAKE_PAR. The direction is "from - to", don't mess this up utherwise the superposition will not be what you expect.

    After you are done, click the FIT_PAIR item, which will perform the superposition according to the provided pair list.

    FIT_DIST

    It is assumed that molecules are more or less superimposed already. So the pair list is generated using a distance criterion [default cutoff is 1.5A] trying to superimpose selected atoms [default atom name is CA] of two provided segment names. List of segment names and wild signs are accepted.

    FIT_SEQU

    When you know that sequence ids of two molecule match use this option. sequence ids will be used to create a pair list, which will be then used in the fitting procedure.

    After the first fitting step the second fit based on a pair list created on a distance criterion always follows.

    MAIN Reference Manuals:SECONDARY File: secondary.txt
    Last modified: 17-jan-2003

    SECONDARY

    Click on a secondary structure item sets conformation of "active" protein main chain atoms to standard helices, beta sheets or other regular patterns. Conformation conversion starts rotating 'active' atoms around predefined bonds from N-(FORWARD) or C-(BACKWARD) terminus, depending whether "FORWARD" or "BACKWARD" flag is set.

    Click the "DIHEDRAL" item requires preceding atom picking and a dihedral value from the keyboard. DIHEDRAL is not limited to some standard atom types and dihedral angle value(s). You can define any dihedral angle among any four atoms you want.

    Clicking standard (1-4 BETA, 1-3 GAMMA) turns items changes conformation of the second and third residue FORWARD or BACKWARD from the last picked residue by 1-4 turns while by 1-3 turn only the second residue conformation is changed.

    All geometry changes are instantaneous, no confirmation is required. "UN_DO" can get you one step backwards. In the case you have messed up everything, you have to extract the last editing session commands from the created "input.cop" file and insert a return command before the command where the mess begun.

    The menu is encoded in MAIN source, so can not be changed.

    For command syntax see MAIN_COM:secondary.html.

    The "SECONDARY" structure elements MENU is placed on the page 8 and shown in violet.

    Secondary structure elements can be applied in block ("HEL_ALPH", "HEL_3-10", "COLLAGEN", "POLI_PRO", "BET_ANTI", "BET_PARA", "EXTENDED") by acting on the "active" selection or as turns ("TURN_I", "TURN_II", "TURN_III" and their "primes"', "GAMMA" and "GAMM_IN"-verse turns) acting on the next four or three residues away from the last clicked atom.

    The model changes conformation "FORWARDS" or "BACKWARDS" from its N-terminus towards C-terminus of a chain or vice versa. Its starting terminus preserves the position.

    MAIN Reference Manuals:SELECT File: select.txt
    Last modified: 27-sept-94

    SELECT

    Keysword: SELECT

    By using SELECT menu items a user is enabled to utilize flexibility of many menu item blocks. By picking the SELECT menu items four KEYs can be accessed ('active', 'pasive', 'image' and 'anchor') and modified by logical operations of the SELECT ... END command sentence. ITEMS including boxes are setup flags, that are at the moment, when a SELECT command item is picked, transformed into a SELECT ... END command sentence specifying a new key definition.

    KEY 'active' is the selection used in most of menu driven actions. KEY 'passive' is used for ENERGY calculations serving as interaction to 'active'. Positions of atoms that are included in KEY 'passive' only and not in KEY 'active' as well, are not modified during an ENERGY MINIMIZATION run.

    KEY 'image' defines pickable atoms from images.

    KEY 'anchor' is the selection used for anchoring atoms by distance constraints, where atoms and their anchors can be moved and minimized separetely. For example picking MIN_ANCH minimizes the anchors in the specified electron density map.

    Tags:

    Tags are organized in three groups each consisting of three items: (SEL_LAST, SEL_RANG, SEL_HIST), (SELE_NAM, SELE_nn, SELE_SEQ) and (SEL_ATOM, SEL_RESI, SEL_MOLE). In each group only a single item flag can be set at a time. A tag is composed by putting together an item of each Tag group in a meaningful entity. The first group flag specifies how many atoms from the history list will enter a tag. The second group specifies wheter atoms will be selected according to names, numbers or sequence names. The third group specifies whether tag refers to atom, residue or a molecule (segment) level of molecular structure organization.

    Setting flags does not affect any key as long an item in the Select group (SELE_ALL, SEL_COPY, SEL_ARO?, SEL.not., SEL .or., SEL_.and.) has been pressed.

    KEY_ACTI

    Sets current SELECTION to the 'active' key.

    KEY_PASI

    Sets current SELECTION to the 'passive' key.

    KEY_IMAG

    Sets current SELECTION to the 'image' key.

    KEY_ANCH

    Sets current SELECTION to the 'anchor' key.

    SEL_CLEA

    
    > key ... select .not. all end
    

    Clears the currently ('...') chosen SELECTION. After this command the chosen selection includes NO atoms.

    SELE_ALL

    
    > key ... select all end
    

    Includes ALL atoms into the currently ('...') chosen selection.

    SEL_COPY

    
    > key ... select active end
    

    Copies the contents of 'active' to the currently ('...') chosen selection ('anchor' or 'image').

    
    > key passive select active .or. by resid by bond active end
    

    The 'passive' selection is thereby also enlarged for the residues, that form a covalent bond with an 'active' atom.

    
    > key active select passive end
    

    In the case when the currently chosen SELECTION is 'active' then the contents of KEY 'passive' is copied to key 'active'.

    SEL_ARO?

    
    > key ... select ... .or. -
    > by resid around key active dist real from image end
    

    Modifies the currently chosen SELECTION. All residues that have at least one atom closer than the specified distance from the active KEY and are included in the KEY image are merged (.OR.) into the current selection. The distance should be typed in to the prompt appearing in the standard input window.

    SEL.not.

    
    > key ... select ... .and. .not. tag end
    

    Modifies the currently ('...') chosen SELECTION so that the logical '.and. .not.' operation is performed.

    SEL .or.

    
    > key .. select ... .or. tag end
    

    Modifies the currently ('...') chosen SELECTION so that the logical '.or.' operation is performed.

    SEL.and.

    
    > key ... select ... .and. tag end
    

    Modifies the currently ('...') chosen SELECTION so that the logical '.and.' operation is performed.

    SEL_LAST

    The chosen tag refers to the last picked atom only.

    SEL_RANG

    The chosen tag refers to the last two picked atoms.

    SEL_HIST

    The chosen tag refers to all picked atoms available in the history list.

    SELE_NAM

    Selects atoms according to (ATOM, RESIDUE or SEGMENT) NAMES.

    SELE_nn

    Selects atoms according to (ATOM, RESIDUE or SEGMENT) NUMBERS. In the case when SEL_MOLE is chosen, there is a slight modification of the common rule (see SEL_MOLE).

    SEL_SEQU

    Selects atoms according to their SEQUENCE names.

    SEL_ATOM

    Selects atoms according to their ATOMic names or numbers.

    SEL_RESI

    Selects atoms according to their RESIDUE names or numbers.

    SEL_MOLE

    Selects atoms according to their SEGMENT names or numbers. In the case of SELE_NAM selection always relates to SEGMENT NAMES, while in the case of SELE_nn, the select sentence depends on the current range mode (SEL_LAST, SEL_RANG, SEL_HIST). When SEL_LAST mode is chosen, a molecule is selected. Molecule is defined as a group of atoms attached to the last picked atom through a network of covalent bonds. In both the other cases (SEL_RANG or SEL_HIST) tag refers to already existing SEGMENT numbers.

    SHOW_KEY

    
    > IMAGE MARK ON
                 OFF
    

    Controls displaying of the currently choosen key atom marks on the image screen.

    ANCHOR

    ANCHOR is an extremly flexible tool that in combination with the energy minimization enables you to model the desired geometry of a molecular model. Anchors are target positions for your atoms. They are pooling their origin atoms towards the desired position without destoring the geometry (bond length, angles, impropers) of a molecular model. Anchors positions can be easyly moved. Each atom can have its anchor.

    When created anchors are displayed as green crosses connected with a line to their origin atoms so that you can always keep track of your atom - anchor pairs. Hiting ANCHOR creates an anchor for each atom included in the key 'anchor'. New anchors are created at positions of their origin atoms. Already existing anchors remain on their positions. Anchors that lose their partner atom (orig atom is not any more included in the key 'anchor') are deleted.

    Anchor positions can be optimized regarding to their correlation within an electron density map (MIN_ANCH). This way a better (real space) fit of your model to an electron density can be derived. MAIN Reference Manuals:SET_WEIGHT File: set_weight.txt
    Last modified: 4-mar-2007

    SET_WEIGHT

    SET_WEIGHT menu block deals with manual as well as automated atom weight (occupancy) assignment.

    Menu block is loaded with teh MAIN_CMDS_NEW:load_set_weights.com.

    WEIGH_0

    Sets the variable "set_weight" to 0 in order to define later dummy atoms by hiting items (WEIG_ATO, WEIG_RES, WEIG_ACT).

    WEIGH_1

    Sets the variable "set_weight" to 0 in order to define later crystallographic scatterers by hiting items (WEIG_ATO, WEIG_RES, WEIG_ACT).

    WEIG_ATO

    Sets the last picked atom WEIGHT to the variable "set_weight" defined by the latest WEIGH_0 or WEIGH_1 command.

    
    > set weight sele numb atom $1 end set_weight
    

    WEIG_SID

    Sets the WEIGHT of all side chains atoms of the last picked residue to the variable "set_weight" as set by the latest WEIGH_0 or WEIGH_1 command.

    WEIG_RES

    Sets the WEIGHT of atoms of the last picked residue to the variable "set_weight" as set by the latest WEIGH_0 or WEIGH_1 command.

    WEIG_ACT

    Sets the WEIGHT of "active" atoms to the variable "set_weight" as set by the latest WEIGH_0 or WEIGH_1 command.

    
    > set weight sele active end set_weight
    

    AUTO_WEI

    Sets weight of the residues of the active selection according to the currently active map at the current contour level. It does not simnply set weights of atoms whether they lie in or out of a density map, but also takes account "a sense" of connectivity.

    In combination with KICK MAPS it will remove the unreliable atoms from phasing by setting their occupancies to zero. Which you can use then in the subsequent map calculation.

    MAIN User`s guide:Setup of depp pages explained Last modified: 28-aug-2006

    Setup of depp pages explained

    What is a menu block and what an item

    A MENU BLOCK is a list of ITEMS separated by an empty space. Items within each block are displayed with the saem color. Each ITEM is the visible string you actually see and can click. When clicked, a command line is submitted to the command sentence interpreter. Complexed commands are written as macros.

    The arrow shape cursos indicates the program awaits new events from the interactive devices (mouse, dials and keyboard).

    When an ITEM is clicked the cursor is changed from an arrow to a clock pointing that MAIN is executing the submitted commands. The arrow shape of the cursor reapears after the commands have been completed.

    Some items have filled or empty squares in front of them. This squares mark their status. Clicking on one of them usually does not result in anything, except the change of the mode reflected by the change of the box. Actions happen by clicking other (not-square-headed) related items within the same menu block, which use these modes as parameters.

    "help" mode is activated by pressing "H" in the image window and indicated by the cursor change into the question mark. When items are clicked in the help mode, their documentation is written into the terminal window and no command is submitted. Another "H" returns clicking of items into the working mode indicated by the "arrow" cursor shape.

    Loading menu blocks

    The file MAIN_CMDS_NEW:load_depp_page.com and MAIN_CMDS:load_depp_page.com (for the older releases) load the initial menu setup. MAIN_CMDS: and MAIN_CMDS_NEW:directories include macros of menu items (".cmds" files) and the "load_...com" files, which load the additional menu blocks. Each menu item command that starts with a "?" checks weather the file with that name is present in your working directory, and when found it is processed, otherwise the default MAIN installation file is taken.

    If you want to create your menus, look at the "load" files as examples and see MAIN_COM:menu.html for further instructions.

    Menu blocks documentation and documentation mode

    Documentation files of menu blocks are stored in MAIN_MENU: directory and are accessible also via MAIN_DOC:dialog_manual.HTML.

    When the "Depp pages" window is in the DOCUMENTATION mode, short description of the pressed BLOCK and ITEM is written to the standard output window. The DOCUMENT mode can be turned on or off either by pressing 'h' on the keyboard or by typing the command

    
    > MENU DOCUMENT ON/OFF.
    

    Using menu items

    Some items require arguments, some don't. The arguments are in passed to an time in a form of

    • history list,
    • atomic selections,
    • strings typed into the starting MAIN window (inquired variables) or
    • somewhere else predefined MAIN variables.

    The general philosophy is that you first define an argument and afterwards activate the function. This way the same argument can be reused in many functions, besides the argument list can be edited so that the atom clicked by mistake can be removed with no need to cancel the function. So approval of a command is not necessary. One level of "UN_DO" for coordinate changes can return the geometry of a model to its previous state.

    This provides a drawback for beginners and an advantage for experienced users: as the arguments are first defined as potential arguments that will turn into applied arguments as a function is activated (an ITEM is clicked) it is for an unexperienced user not immediately clear which form and which potential argument will be taken with a certain function. So browsing the manual can be of help - in particular the documentation related to the menu items in "Dialog Mode Accessories" manual (MAIN_DOC:dialog_manual.HTML).

    Menu arguments: History list

    Atoms are arguments. more precisely they become potential arguments, by clicking. When clicked, an atom is pushed on the top of the history list. The last one clicked is always the first one on the list. The last atom can be dropped from the list ("HIS_DROP"). The whole history list can be erased with "HIS_ERAS". The "HIS_DIST" allows you to measure and monitor interatomic distances when moving the atoms around. For more about history items see MAIN_MENU:history.html.

    "IMAGE HISTORY" commands manipulate the history list and history functions. See MAIN_COM:image.html.

    Menu arguments: Selection keys

    The history list is created by clicking atoms. Atomic selections are usually created by providing history atoms to the "SELECT NICE" and "SELECT LONG" menu blocks. You can, however, at any moment choose to use the command language to define or redefine any of the keyed arguments. The most commonly used keys are "active", "passive" and ""image"".

    Key "active" tells that something will happen with the selection of atoms (MINIMIZE, for example, will allow to move only active atoms). the key "image" contains the list of pickable atoms, ...

    "KEY something SELECT ... END" commands manipulate the keys. See MAIN_COM:select.html.

    There is also "WORK_REFL" key, which does not mark a list of atoms but reflections. It is a key, in contrast to "WORK_SEGM", which is a variable.

    Menu arguments: inquired variables

    Some arguments are inquired. You have to respond with a typed an answer, which can be either an integer or real number or a string. The resulting variables are either immediately applied ("LOAD_PDB") and also deleted after their use, or stored as GLOBAL variables to be used later in combination with other items ("MAP_ACT" and other map related menu items). Command

    
    > show vari
    

    reveals the current variable list and their values. For instructions how to set variables see "SET VARIABLE" in MAIN_COM:set.html.

    Menu arguments: predefined variables

    Some variables are defined in the initial macros as global variables and then used throughout the MAIN macros environment to pass some common arguments.

    The variable "WORK_SEGM" contains a list of working SEGMENT NAMES. It is used to pass the list to various macros, which then use the list in their SELECT commands. "RE_IMAGE", "SYMMETRY", "REFINE" are only some of such menu items. The variable is defined in a "read.com" file and can be verified with "SHW_SEGM" updated with "UPD_SEGM" menu items. If the variable doesn't exist, or contains the wrong segment names, essentially nothing will work, unless you have created your own environment almost entirely.

    In a "read.com" map variables "MAP_2FOFC", "MAP_FOBS" are defined in order to differentiate among various created maps.

    The "DEF_ALL" variable is defined in a MAIN_UTILS:get_top_par_19_csd.com or similar script and it points to a macro, which assigns atom types and creates lists necessary for energy calculations.

    MAIN Reference Manuals:SHORT_ENERGY File: short_energy.txt
    Last modified: 3-feb-97

    SHORT_ENERGY

    The SHORT_ENERGY menu comprises the extended ENERGY menu block into four items, where all CHEMISTRY energy terms (bonding and nonbonding including hydrogen bonds) can be truned on and off with a single click. The DENSITY and ANC-PAIR (anchor and pair) energy terms can be still handled independently. MAIN Reference Manuals:TRACE File: trace.txt
    Last modified: 5-mar-2007

    TRACE

    Menu block "TRACE" contains items, which perform automated model building and chain tracing. User has to choose the range of a function application: working segment, key active or clicked history atoms.

    Menu block "TRACE" is loaded with MAIN_CMDS:load_trace.com.

    See also MAIN_DOC:build/new_struc.html.

    GOTO_SKEL

    Redraws a previously generated skeleton in order to enable its manual editing.

    GOTO_HYB

    Redraws a previously generated skeleton and the hybrid model in order to enable the hybrid model manual rebuilding, minimization, refinement of phasing.

    GOTO_ALA

    Redraws the current polya ALA model.

    RoH_JOBS

    Robert Huber jobs.

    This is a single click function, which combines all steps of automated model building. It is not really implemented yet.

    Configure it with the MAIN_CONF:create_roh_jobs.pl.

    TRC_ORIG

    Locates adjacent origin(s) of molecule(s).

    GEN_SKEL

    Generates skeleton around the current selection with box expanded 15 grid points from the current active map.

    RE_SKEL

    Re-generates skeleton in the same box as defined baove only at different contouring level.

    TRC_SKEL

    Assignes secoondary structure elements and connections to skeleton. Secondary structures are yellow, main chain straces green.

    TRC_HYBR

    Repeats the "TRC_SKEL" step and builds hybrid model (sp3 fragments) along the main chain trace.

    MAIN_CMDS:trace_3angl.cmds macro does it.

    TRC_ALA

    Build poly alanine model along the hybrid model.

    MAIN_CMDS:trace_chain.cmds macro does it.

    TRC_SYMM

    Moves fragments around applying crystal symmetry operators to position them into a asymmetric unit.

    MAIN_CMDS:trace_symm_overlaps.cmds macro does it.

    TRC_MERG

    Merge overlapping fragments into the best unique trace.

    This is still work in progress.

    TRC_SIDE

    Trace side chains - find the best residue fitting the density and geometry constraints.

    Currently only amino acid residues are supported.

    MAIN_CMDS:trace_side.cmds macro does it.

    MAIN Reference Manuals:UN_DO File: un_do.txt
    Last modified: 24-feb-2007

    UN_DO

    UN_DO

    UN_DO swicthes forward and backwards between the current and backup coordinate sets allowing instant "undos" of geometrical changes.

    Before activation of each change coordinates are backuped.

    For going several steps backword either the file "input.cop" has to be edited for ecovery. In most cases restore ("REST_FIL") coordinates from the "save files" will do.

    Shortcut is "u". MAIN Reference Manuals:USE_ATOMS File: use_atoms.txt
    Last modified: 27-sept-2002

    USE_ATOMS

    Three items are three modes defining the range of atoms on which automated procedures (MAIN_MENU:auto_stuff.html, MAIN_MENU:trace.html) are applied.

    USE_WORK

    Procedures will be applied on segments names included in the variable "WORK_SEGM".

    To inspect the contents click "SHOW_SEG" on page 9.

    USE_ACTI

    Procedures will be applied on the "active" key atoms.

    USE_HIST

    Procedures will be applied on the last one or two clicked atoms from the history list.

    MAIN Reference Manuals:UTILS File: utils.txt
    Last modified: 16-jan-2003

    UTILS

    The utilities macros are a sample of generally useful routines with no common denominator. They all are placed in the MAIN_UTILS: directory.

    The menu is loaded with MAIN_CMDS:load_utils.com.

    LOAD_PDB

    You are prompted for a PDB file that is read, covalent bonds are calculated and displayed with the MAIN_CMDS:re_image_set.cmds macro. The center of the image is placed into the middle of the molecule.

    The macro is MAIN_UTILS:load_pdb.com.

    READ_ATO

    You are prompted for root of a PDB file that is then read. Connectivity table file with extension ".ctab" is read as well. "READ_ATO" reads what is saved with "SAVE_AS".

    The macro is MAIN_UTILS:read_atom.com.

    BACK_PDB

    Loads a background image of a pdb file. You are prompted for a PDB file, which is processed as in the LOAD_PDB, displayed with a re_image_col.cmds macro (in one color) and stored into the background.

    The macro is MAIN_CMDS:utils_background_pdb.cmds.

    CALC_BON

    Calculate covalent bonds. It affects segments names with their names included into the WORK_SEGM.

    The macro is MAIN_UTILS:calculate.bonds.

    FILL_ATO

    Fills the missing atoms into the residues according to their description in the topology library. Useful also for hydrogen insertion. It affects segments names with their names included into the WORK_SEGM.

    Be careful - the N and C- terminal atoms HTn may disappear. OXT however stay.

    The macro is MAIN_UTILS:fill_atoms.com.

    xpl2MAIN

    xpl2MAIN does a simple renaming of atom and residues from an X-PLOR pdb standard to MAIN. The most common mismatches between X-PLOR and MINA are in, but it will not fix all the things It affects segments names with their names included into the WORK_SEGM.

    The macro is MAIN_UTILS:xplor_2_main.com.

    MAIN2xpl

    MAIN2xpl is the reverse conversion from the xpl2MAIN. It will not fix everything, but generally may work. It affects segments names with their names included into the WORK_SEGM.

    The macro is MAIN_UTILS:main_2_xplor.com.

    LIB_PROT

    Reads the topology library and parameter file from the CSD (Engh \& Huber) force field.

    The macro is MAIN_UTILS:get_top_par_19_csd.com.

    LIB_NU-P

    Reads the topology library and parameter file from the CSD (Engh \& Huber) force field and DNS library.

    The macro is MAIN_UTILS:get_top_par_prot_dna.com

    LIB_CHO

    Reads the topology library and parameter file for carbohydrate (sugar)rings.

    The macro is MAIN_UTILS:get_top_par_sugar.com

    TRP_2_W

    Converts amino residue names into the single letter code.

    The macro is MAIN_UTILS:ren_to_1_let_code.com.

    W_2_TRP

    Converts amino residue names from the single letter code to the 3 letter code.

    The macro is MAIN_UTILS:ren_from_1_let_code.com.

    SAVE_AS

    Saves the current WORK_SEGM into atom coordinates and connectivity table files.

    The macro is MAIN_UTILS:save_as.com.

    RE_ORDER

    Reorders residues in all segments part of WORK_SEGM so that amino residues follow the peptide bond connections. Chain and sequence IDs are automatically reassigned. Sequence IDs of each residue startswith the chain ID and followes by the consecutive number of the position in the chain.

    The MAIN_UTILS:re_order_chains.com does it.

    RAMACHAN

    Displays the framework and graph of a Ramachandran plot and attaches dials to it manipulation.

    The macro is MAIN_UTILS:rama.com.

    RAMA_PRO

    Displays Ramachandran diagram of a protein. Segments names with their names included into the WORK_SEGM are used.

    The macro is MAIN_UTILS:rama_prot.com.

    SHOW_CEL

    SHOW_CEL displays a crystal lattice of 4x4x4 unit cells.

    The macro is MAIN_UTILS:show.cell.

    LOAD_FON

    Loads 8 X-window server fonts of different size.

    Command

    
    > image font use 3
    

    specifies the use of font number 3.

    The macro is MAIN_UTILS:load_fonts.com. MAIN Reference Manuals:XRAY_BUILD File: xray_build.txt
    Last modified: 27-may-98

    XRAY_BUILD

    The functions herein support model building in electron density. It enables you to reconstruct image on the screen (RE_IMAGE), to create and display symmetry related molecules (SYMMETRY, SYMM_CA), set crystallographic weights to atoms (WEIG_ATO, WEIG_RES, WEIG_ACT), find symmetry equivalent segments of your current model (WHERE_IS), and change coordinates of your model segment by a symmetry equivalent one (COPY_COO). UN_DO returns your model coordinates one step back.

    All cmds files are available in the MAIN_CMDS: directory. These are processed unless you provide your own replacement in your current working directory.

    The SAVE command should save your current data to files. Write your own "save_file.cmds"!

    This menu BLOCK is loaded with the command MAIN_CMDS:load_xray_build.com.

    RE_IMAGE

    The RE_IMAGE macro erases entire image and displays covalent bonds and hydrogen bonds of segment names included in the WORK_SEGM variable. The atoms not covalently attached to any other atoms are displayed as atom crosses.

    The default macro is the MAIN_CMDS:re_image.cmds file. If a 're_image.cmds' file is present in your current working directory then this file processed by clicking the RE_IMAGE item. Segment names are submitted through a properly assigned WORK_SEGM variable to the macros.

    You are encouraged to write your own "re_image.cmds" files.

    There a high chance for a beginners surprice: your molecules do not show up on the screen also after 1000 clicks of the RE_IMAGE. The WORK_SEGM variable was not defined. (Menu page 8, item UPD_SEGM may comfort you.)

    SYMMETRY

    The SYMMETRY command generates symmetry related molecules within a specified radius from the last clicked atom. Default radius is 20 AA. The default file is MAIN_CMDS:symmetry.cmds. If you have a "symmetry.cmds file present in your working directory, that file will be processed.

    Segment names are passed via the variable WORK_SEGM.

    If you want to differentiate between different molecules or subunint present by a color then you should definitely use your own symmetry.cmds file.

    SYMM_CA

    The SYMM_CA command generates packing of nearby laying symmetry related molecules within a specified radius from the last clicked atom. CA connections are shown. Default radius is 50 AA. The default file is MAIN_CMDS:symmetry_ca.cmds. If you have a "symmetry_ca.cmds" file present in your working directory, that file will be processed.

    Segment names are passed via the variable WORK_SEGM.

    If you want to differentiate between different molecules or subunint present by a color then you should definitely use your own symmetry.cmds file.

    UN_DO

    Restores atomic coordinates to the values before the last MINIMIZATION, SECONDARY structure change or geometry changes (ROT_TRAN, RT_CHAIN .... CONNECT, REFINE) click.

    Msotly applied after "MINIMIZE", because a "DEFINE" was forgotten.

    WEIGH_0

    Sets the variable "set_weight" to 0 in order to define later dummy atoms by hiting items (WEIG_ATO, WEIG_RES, WEIG_ACT).

    WEIGH_1

    Sets the variable "set_weight" to 0 in order to define later crystallographic scatterers by hiting items (WEIG_ATO, WEIG_RES, WEIG_ACT).

    WEIG_ATO

    Sets the last picked atom WEIGHT to the variable "set_weight" defined by the latest WEIGH_0 or WEIGH_1 command.

    
    > set weight sele numb atom $1 end set_weight
    

    WEIG_RES

    Sets the WEIGHT of all non hydrogen atoms of the last picked residue to the variable "set_weight" as set by the latest WEIGH_0 or WEIGH_1 command.

    WEIG_ACT

    Sets the WEIGHT of "active" atoms to the variable "set_weight" as set by the latest WEIGH_0 or WEIGH_1 command.

    
    > set weight sele active end set_weight
    

    TEMP_ACT

    Sets the TEMPERATURE factor of "active" atoms to the value you should type in on the keybord.

    WHERE_IS

    Displays with white bonds all equivalent residues (with identical sequence names) of the segment you have just picked.

    The procedure is in file MAIN_CMDS:where_is_segment.cmds.

    COPY_COOR

    Copies coordinates of the segment you have just picked (a symmetry equivalent segment) to the original model. With this command you can move atoms around through symmetry equivalent positions you find on the screen. Useful especially when you realize that a segment should move to another asymetric unit (by model building or a molecular envelope construction).

    Use this item only in combination with SYMMETRY generation.

    The procedure is in the file MAIN_CMDS:copy_coor.cmds.

    INV_CHAIN

    Inverts direction of a peptide chain (KEY "active") by keeping the initial secondary structure (phi, psi angles) as close as possible to the original values.

    The procedure is in the files MAIN_CMDS:invert_chain.cmds and the fitting parts in MAIN_UTILS:invert_chain_rms.com.

    SAVE

    SAVE saves atom data, current connectivity table and the current view. SAVE is supposed to be a security measure. In a "read.com", the starting MAIN file, you should not use the same files as specified in your "save_file.cmds".

    Before starting MAIN copy these files to the files MAIN will actually read at the beginning. In the case of corrupted save files you may find yourself in a big trouble. Restavration of the last editing session may not be possible any more.

    The save view command is only to make life easier. It does not effect any structural data so you can easily process it during your starting file (read.com). It doe snot hurt if you keep using the same name for saving the current view and staring a view macro.

    Hint: Create SAVE_2 item so that you keep two file tracks.

    
    > menu block XRAY_BUILD item SAVE add text "<save_file.cmds"
    

    The default MAIN_CMDS:save_file.cmds:

    
    > subroutine char SEGMENTS
    > write over file SAVE_FILE.PDB select segment name SEGMENTS end atom pdb
    > write over file SAVE_FILE.CTAB select segment name SEGMENTS end ctab
    > save over file SAVE_FILE.VIEW view
    > return
    

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