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.
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.)
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.
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.
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.
Sets the variable "set_weight" to 0 in order to define later dummy atoms by hiting items (WEIG_ATO, WEIG_RES, WEIG_ACT).
Sets the variable "set_weight" to 0 in order to define later crystallographic scatterers by hiting items (WEIG_ATO, WEIG_RES, WEIG_ACT).
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
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.
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
Sets the TEMPERATURE factor of "active" atoms to the value you should type in on the keybord.
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.
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.
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 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