ListSelection2
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Type | Python Script |
---|---|
Download | figshare |
Author(s) | Pietro Gatti-Lafranconi |
License | CC BY 4.0 |
Overview
Alternative script to List_Selection that will:
- list multiple residues once
- include water and hetatoms
- account for different chains/objects
- produce a screen/printed output
Usage
listselection selection, [output=N/S/P, [HOH=Y/N ]]
where:
- selection can be any existing or newly-defined selection
- output controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
- HOH (default Y) allows to exclude (N) water residues from the list
Examples
PyMOL>listselection 1efa, output=P
Residues in '1efa': 1043
Results saved in listselection_1efa.txt
PyMOL>listselection sele, output=S, HOH=N
Residues in 'sele, without HOH': 7
1LBH/A/ARG/86
1LBH/A/ALA/87
1LBH/A/ASP/88
1LBH/A/GLN/89
1LBH/A/LEU/90
1LBH/A/GLY/91
1LBH/A/ALA/92
PyMOL>listselection 1efa and resn LEU, output=S
Residues in '1efa and resn LEU': 108
1efa/A/LEU/6
1efa/A/LEU/45
1efa/A/LEU/56
[...]
1efa/C/LEU/323
1efa/C/LEU/330
Code
Copy the following text and save it as listselection.py
from pymol import cmd, stored
def listselection (selection, output="N", HOH="Y"):
"""
usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]
More information at: PymolWiki: http://http://pymolwiki.org/index.php/ListSelection2
AUTHOR: Pietro Gatti-Lafranconi, 2013
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""
printedselection=""
extra=""
counter=0
sel=selection
objs=cmd.get_object_list(sel)
if HOH=="N":
sel=selection+" and not resn HOH"
extra=", without HOH"
for a in range(len(objs)):
m1=cmd.get_model(sel+" and "+objs[a])
for x in range(len(m1.atom)):
if m1.atom[x-1].resi!=m1.atom[x].resi:
printedselection+="%s/%s/%s/%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resn, m1.atom[x].resi)
counter+=1
print "Residues in '%s%s': %s" % (selection, extra, counter)
if output=="S": print printedselection
if output=="P":
f=open('listselection_'+selection+'.txt','w')
f.write("Residues in '%s%s': %s\n" % (selection, extra, counter))
f.write(printedselection)
f.close()
print "Results saved in listselection_%s.txt" % selection
cmd.extend('listselection',listselection)