File: center.txt


Last: modified: 13-apr-2019

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


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


Sets the current center to last clicked one.


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.


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.
  -h|--help)      prints this message with available options and current status
  -o|--output)    set file name of the created macro [anal_center_list.cmds]
  -f|--field)     validation field to be examined [AVERAGE/RMS/MIN/MAX/BOTTOM/TOP] [AVERAGE]
  -c|--cutoff)    sigma cutoff value for the list creation [3]
  -t|--top)       the top violators [50]
  -m|--map)       map for analysis [1/2/3/4/5/6/7/8/9/10] [2]
  -a|--atom)      atom list PDB file [atom_list.pdb]
  -g|--group)     groups of selections [ACTIVE/WORK_SEGM/SELECTION] [ACTIVE]
  -s|--selection) atom selection [.n all]
  -k|--task)      additional task [NONE/MINIMIZE/FIT_SIDE/AUTO_FIT/PICK_ATOM/MY_TASK] [NONE]
--doit)      create the macro "anal_center_list.cmds"

Using the "configure" mouse button (right), the "" 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 "" and creates the "" macro, which contains the sorted list of violators of your analysis.