Last modified: 18-oct-2007
The SET command sentences are used to SET some values or parameters relevant for atomic records (B_VALUES, WEIGHTS, COLORS, RADII, COORDINATES, SECONDARY - these modules can be entered also from MAIN directly), GEOMETRY relations, they control DIALS assignment and parameters relevant for general MAIN control (VARIABLES, LEVEL, MATRIX, CENTER)...
SET B-VALUES BOND ATOMS FORWARD 3*atom-num BACKWARD POINTS CHRAGES LEVEL inte DIALS ..... DISPLAY int1 int2 int3 int4
VARIABLE string real/inte/string
! AUTODIALS inte INITIALIZE ! STEP real ! TIME_STEP realMATRIX int0 INITIALIZE X-AX real (in degrees) Y-AX real Z-AX real NUMBERED 9 * real * inte \ inte DEORTHOGONAL ORTHOGONAL SYMMETRY inte TRANSPOSE INVERSE COPY RMS POLAR_ANGLES 3*real (psi, phi, kappa) or (phi, psi, kappa) ATOM atom-num atom-num atom-num
PLANE ATOM atom-num1 atom-num2 atom-num3 NUMBERS 4*real SELECT ... END INITIALIZE DROP [inte]
RMS 3*real 3*real
RIBBON AUTOMATI COIL DENSITY real EXIT HELIX INITIALI N_LINES int RADIUS real REFINE int SELECT ... END SEPARATI STEPS int STRAND
STICK DENSITY int RADIUS real
CENTER ATOM atom-num CALCULATE [SELECT ... END] COORDINATES 3*real SEQUENCE string POINT inte
INVERSE/CHANGE atom-num1 atom-num2
GEOMETRY DISTANCE 2*atom-num ANGLE 3*atom-num DIHEDRAL 4*atom-num INTERNAL_COOR 4*atom-num ALIGN 2*atom-num VALUES real [real real] AUTO SELECT ... END
... LEVEL inte
Sets the message level (errors, warnings, debugging data). A lower value results in fewer messages and a higher in more. The starting LEVEL value is 0. You can set any number, also only values between -5 and 5 differ in effect.
... DIALS inte TRANSLATION  X-AX Y-AX Z-AX CENTER () X-AX Y-AX Z-AX SCALE CLIPPING ROTATION  VIEW SCREEN STEREO ANGLE XCENTER COLOR inte string INITIALIZE CHARACTER OBJECT inte BOND ANGLE DIHEDRAL DISTANCE ROTATION X-AX Y-AX Z-AX TRANSLATION X-AX Y-AX Z-AX READ WRITE IMAGE_PARAMETERS DROP GRAPH TEXT string OBJECT inte TRANSLATE ALL X-AX Y-AX Z-AX SCALE ALL X-AX Y-AX Z-AX CHARACTER ROTATE ALL X-AX Y-AX Z-AX FROM inte
SETs the DIAL definitions. The DIALS are not set through an IMAGE command sentence to allow the use of a single command word (DIAL) to enter the DIAL-OG mode and to assign functions to DIAL-S. Most dial definitions are governed by the program itself or can be picked from menus when MAIN is in the DIALOG mode. Each DIAL has a label, that tells what is the function of the dial and to which object it is attached (in the case of OBJECT and GRAPH DIALS). Sometimes it is necessary to do DIAL_SAV from menu so as not to lose some dial definitions. Up to 10 different dial sets can be stored and restored. A dial set is a combination of 8 dial functions.
It is called using DIAL_RST menu item (dial restore) in DIALOG mode. It READS (restores), the next dial set from the list. So one after another all the saved dial sets can be restored.
It is called using DIAL_SAV menu item (dial save) in DIALOG mode. It WRITES (saves), the current dial set to the list. The dial set is stored as last and the pointer is moved to it. The rule is written last, read first.
DROPS (forgets) all dial definitions to the consecutive number inte2, that is set by the SET DIAL inte FROM inte2 command. (It sets the list count to inte2. By default this number is equal to 0.) It is called automatically when the current geometry of the active OBJECTS is accepted (OBJ_ACCEP) or rejected (OBJ_REJEC) in DIALOG mode.
... FROM inte2
Protects the dial set definitions as saved on the list from deletion, by SETing the lowest value to which the dial set count can be DROPPED. By default it is set to 0, which means none of the dial sets is protected. This command is used for example to protect the Ramachandran plot GRAPH manipulation during a model building session.
... TRANSLATION  X-AX Y-AX Z-AX
Sets 3  or a single DIAL to transfer the translations of the image in X, Y or Z direction. The rotation center of the image remains unchanged and may even move out of the screen.
... CENTER  X-AX Y-AX Z-AX
Sets 3  or a single DIAL to control the translation of the rotation center of the image in X, Y or Z direction. The rotation center remains all the time in the middle of the screen, so the image is shifted. (This is the default.)
Controls SCALING of the IMAGE. The value should be negative for the PSnnn devices, since their coordinate system is left-handed.
Controls the distance between the two CLIPPING planes. CLIPPING of the image occurs in the Z direction.
... ROTATION  X-AX Y-AX Z-AX
Sets 3  or a single DIAL to control the rotation of the image around the rotation center in X, Y or Z direction.
Controls distance from the VIEWER eye position to the center of the image. MAIN uses perspective view.
Controls the distance between the VIEWER to the imaginary SCREEN on which the image objects are projected. In GL or OpenGL environment this parameter is related to the field of view.
... STEREO ANGLE XCENTER
Controls the STEREO ANGLE and separation (XCENTER) of the image rotation centers along the X axes for side by side stereo.
... COLOR inte string
A dial controls color of an image object. A dial is defined in DIALOG mode by first activating the color mode and then clicking an image object.
Restores the INITIAL definition of the DIALS (X,Y and Z center translations, scaling, X, Y and Z axes rotations and clipping).
Controls the character size.
... OBJECT inte ...
The active OBJECTS of MAIN are the SELECTIONS of atoms on which particular functions are activated in order to control the spatial changes of molecules interactively. When an OBJECT is activated from the DIALOG mode the DIALS are assigned to it automatically.
... BOND ... ANGLE ... DIHEDRAL ... DISTANCE ... ROTATION  X-AX Y-AX Z-AX ... TRANSLATION  X-AX Y-AX Z-AX
The assigned DIAL rotates a BOND, changes an ANGLE, a DIHEDRAL angle, moves along the vector connecting the last twoclicked atoms (DISTANCE). Three DIALS are assigned to ROTATE around all 3 axes or only one DIAL to ROTATE around one (X-AX or Y-AX or Z-AX). Definitions for the TRANSLATION of the OBJECT follow the same rules as the ones for ROTATION.
SETs the view parameters DIAL set. (1-SCREEN, 2-VIEW,
ANGLE, 4-STEREO XCENTER, 8-CHARACTER scale)
... GRAPH ...
Controls the GRAPH objects (TEXT - translations inside a GRAPH OBJECT) and a GRAPH OBJECT as a whole. (Its orientation, translation and scaling.)
... TEXT string
String is a name of an IMAGE object.
... OBJECT inte
... TRANSLATE ALL X-AX Y-AX Z-AX
TRANSLATION of a GRAPH OBJECT assigned with ALL, defines 3 DIALS, one for each direction, while the X-AX, Y-AX or Z-AX define 1 DIAL for each separate direction.
... SCALE  X-AX Y-AX Z-AX ALL
SCALING of a GRAPH OBJECT can be coupled (ALL), which means that SCALING in ALL three directions is the same, and is governed with a single DIAL. Each axis can also be scaled independently (X-AX, Y-AX, Z-AX) using one DIAL per axis. With no () explicit specification four DIALS are assigned, one for each of the possible SCALING controls.
Controls the CHARACTER size of the GRAPH OBJECT. Only works under PHIGS graphics interface (on HP and ESV systems).
... ROTATE ALL X-AX Y-AX Z-AX
The ROTATION of a GRAPH OBJECT is controled along each axes (X-AX, Y-AX, Z-AX). If you want to adress rotation about ALL three of them similtaneously use command ALL intstead of three separate dial definition commands.
,,, int1 int2 int3 int4
The four integer values may override deafult size and origin position of the windows during the image initialization. The first pair defines the uper left corner of the image window, whereas the second pair defines the maximal size of dislpay available for the application. When X-server sizes are smaller than the user defined ones, the X-server default values prevail.
... VARIABLE string0 REAL INTEGER CHARACTER LOCAL GLOBAL = inte/real/string1 SEGMENT SELECT ... END RESIDUE SEQUENCE ATOM
SETs the VARIABLE adressed with the string0 to a value that can be either an INTEGER, a REAL number or a CHARACTER string. The program normally recognizes the kind of VARIABLE from the argument. You are however advised to explicitly specified the type. Variables can be assigned as GLOBAL or LOCAL ones. The GLOBAL are seen throughout of the program run, while the LOCAL ones exist only on the particular macro level. A RETURN deletes them.
Values of character variables can be extracted from a selection of SEGMENT, RESIDUE or ATOM NAMES and SEQUENCE IDs.
Integer number can be extracted from the first selected ATOM, RESIDUE or SEGMENT.
The variables can be further applied in any command sentence at the place of required input data (integer or real numbers and strings). The only exception is this command sentence, where the string0 is assumed to be the variable name explicitly and not its value. The VARIABLE name string0 can be any string up to 10 characters long. Character variable values can be up to 80 characters long.
See sections "INQUIRE" and section "DELETE VARIABLE".
> inquire real global variable XX text "GIVE ME A REAL NUMBER:"
... DENSITY int RADIUS real
SETS the stick RADIUS and DENSITY (number of circle divisions).
... BOND ATOM FORE atom-num atom-num atom-num POINT BACK
BOND FORE atom-num atom-num transforms the atom coordinates so that the specified BOND is in direction of the X axes and with the origin at the first specified atom. BACK does the opposite transformation. It returns only one level back.
Using two consecutive BOND FORE commands without the BOND BACK command in between, the user can not return to the original coordinate system any more.
... MATRIX int0 INITIAL X-AX real / in degrees Y-AX real Z-AX real NUMBERED 9 * real * inte \ inte INVERT TRANSPOSE DEORTHOGONAL ORTHOGONAL POLAR_ANGLES phi psi kappa (or phi psi kappa) SYMMETRY inte COPY inte RMS ATOM atom-num atom-num atom-num
MATRICES int0 (1 to 8) can be set. MATRIX 1 and 8 are used for the image processing (8 is the stereo pair). MATRIX 6 is the matrix that is used to define a rotation around a single axis (X-AX, Y-AX, Z-AX).
MAIN> set mat 3 init x-ax 3. y- 45. z- 90. y- -34. z- 3.45 y- 1890.
will result in matrix 3 that is composed of the 6 specified rotations. Matrices can be defined explicitly by NUMBERED input of the 9 consecutive real numbers. MATRICES can be COPIED, INVERTED, TRANSPOSED, multiplied (*), divided (/), INITIALIZED (set to a unit matrix), specified by the POLAR angles or by symmetry operations, or as DE/ORTHOGONALIZATION matrices or calculated from the last RMS fit rotational parameters.
WARNING: Whenever you transfer or interchange matrices between various programs you do always have to check the consistency of matrix definitions. They should be all the same but they are not!!!
Sets all program variables and data to the initial state (ONLY ATOMS AND COVALENT BONDS ARE LEFT). Don't use it unless you are really in trouble because of a bug.
!2 POINTS !POINTS inte PASCAL ! TRIANGLE ! SURFACE ! ! Sets the level in pascal triangle rule generation ! for points on the atom surface.
... PLANES ATOM iatom iatom iatom NUMBERED 4*real SELECT ... END INITIALIZE DROP (inte)
ATOM creates a plane through the first three SELECTED atoms. NUMBERED requires the normal to the plane (a, b,c) and the d. [ a*X + b*Y + c*Z + d = 0 ]
SELECT ... END creates a plane that goes through 3 first atoms in selection. (will be used to calculate the RMS plane)
INITIALIZE the number of planes to 0. 10 is maximum.
DROP (inte) one or more plane from the stack.
its place with the last one on the list
... INVERT atom-num1 atom-num2
Interchanges positions of the two atom chains at a chiral center. (INVERTS the chirality). The chiral center atom is the atom to which both specified atoms (atom-num1 and atom-num2 ) are attached by a covalent bond. Each atom chain includes all atoms connected via covalent bonds to atoms atom-num1 or atom-num2 apart from the chiral center.
... GEOMETRY DISTANCE 2*atom-num ANGLE 3*atom-num DIHEDRAL 4*atom-num INTERNAL_COOR 4*atom-num ALIGN 2*atom-num VALUES real [real real] AUTO SELECT ... END
It is the default option. The desired parameter (DISTANCE or ANGLE) is searched in the forcefield parameter library.
... VALUES real [real real]
The neccessary number of target values is hereby explicitly defined. One VALUE for BOND, ANGLE, DIHEDRAL and three values for INTERNAL coordinates need to be specified. DISTANCES are in AA and angles in degrees.
... SELECT ... END
By default only the first specified atom is moved, the others are used as reference points only. If you want to move SELECTIONS you have to specify them explicitly.
... DISTANCE 2*atom-num
Moves the SELECTION in the direction of the vector going from atom-num1 to atom-num2, for the DISTANCE that is the difference between the specified real and the distance between the atom-num1 and atom-num2. The specified real can also be a negative value. When atom-num1 is a part of the SELECTION the resulting distance between the atoms atom-num1 and atom-num2 is the specified real. When AUTO is chosen instead of an explicitly defined VALUE then the required distance is searched in the list of BOND ENERGY parameters (according to the atom CLASSES).
... ANGLE atom-num1 atom-num2 atom-num3
Rotates the SELECTION around the normal to the plane defined by the atoms atom-num1/2/3 and going through atom-num2. The ANGLE of rotation is calculated so that when the atom-num1 is included in the SELECTION, the resulting angle between atoms atom-num1/2/3 is the specified real. When AUTO is chosen instead of an explicitly defined VALUE, the required angle is searched in the list of ANGLE ENERGY parameters (according to the atom CLASSES).
... DIHEDRAL atom-num1 atom-num2 atom-num3 atom-num4
Rotates the SELECTION around the bond atom-num2 atom-num3. The angle of rotation is calculated so that when the atom-num1 is included in the SELECTION, the resulting DIHEDRAL angle between the atoms atom-num1/2/3/4 becomes equal to the specified real. When AUTO is chosen instead of an explicitly defined VALUE, the required dihedral angle is set to 180o.
... INTERNAL atom-num1 atom-num2 atom-num3 atom-num4
It combines the translation and rotations of the SET DISTANCE, ANGLE and DIHEDRAL angle into one entity. For description see SET DISTANCE, SET ANGLE and SET DIHEDRAL. Its VALUES parameter however consist of 3 real numbers meaning a distance andgle and dihedral angle.
... ALIGN 2*atom-num
ALIGNS two atoms or a SELECTION so that the two appear to each other at the specified (or bond) distance with their attached neighbors at a reasonable geometrical criteria. It as a construction that may not always work.
... RMS 6*real
SETs the rotational and translational parameters that are usually obtained via the RMS COORDINATES ALL ... procedure. The first 3 parameters are the rotational angles around the X-axes, Y'-axes and X"-axes and the second 3 parameters are the translational vector"the translational vector.
... CENTER ATOM atom-num CALCULATE [SELECT ... END] COORDINATES 3*real SEQUENCE string POINT inte
SETs the CENTER (also IMAGE center) coordinates:
(the coordinates of the CA atom are chosen. When the residue has no CA atom, then the first atom appearing in the chosen residue),
See under the same keyword directly from MAIN (MAIN_COM:temp.html).
See under the same keyword directly from MAIN (MAIN_COM:temp.html).
See under the same keyword directly from MAIN (MAIN_COM:coord.html).
See under the same keyword directly from MAIN (MAIN_COM:radii.html).
See under the same keyword directly from MAIN (MAIN_COM:ribbon.html).
See under the same keyword directly from MAIN (MAIN_COM:weight.html).
See under the same keyword directly from MAIN (MAIN_COM:secondary.html).