2 CENTER
Keyword: center, list, remap, recontour, define
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".

3 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".

3 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".

3 CENT_STA

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

3 CENT_DEF

Sets the current center to last clicked one.

3 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.

3 GEN_LIST
Keyword: validation, 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.

 create_anal_center.pl 
  -h|--help)      prints this message with available options and current status 
  -o|--output)    set file name of the created macro [anal_center_list.cmds]
  -b|--by)        by [GEO_BOND/GEO_ANGLE/PACK/PACK_SYM/DENSITY/ENE_VDW/ENE_MAIN_CHAIN/CIS_PEPT/ROTAMER/PLANARITY/B-VALUE/LOW_MAP_PEAKS/HIGH_MAP_PEAKS/ION_LIST/ATOM_LIST/FILE] [GEO_BOND]
  -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
"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.