ListSelection2
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
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': 5
2P9H\A\101\ARG
2P9H\A\102\SER
2P9H\A\103\GLY
2P9H\A\104\VAL
2P9H\A\105\GLU
PyMOL>listselection 1efa and resn LEU, output=S
Residues in '1EFA and resn LEU': 108
1efa\A\6\LEU
1efa\A\45\LEU
[...]
1efa\C\323\LEU
1efa\C\330\LEU
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 ]]
"""
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].resi, m1.atom[x].resn)
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)