Hi everyone,
How to write PyMol commands in Python script, save a session and then save a
.png file of the same ?
I have an input file which has the protein information i.e name, chain, and a
list of residues.
I want to plot the C-alpha atoms of these residues for each protein & calculate
distances between this set of atoms, save these operations in a .pse file and
also a .png file of the same.
Below, I am writing all the commands which I use in PyMol.
However, I am having trouble automating this procedure for a large number of
proteins.
***Input file [testpy.txt](Fields: PDB ID, chain, residue1, residue2,
residue3***
2YYI.pdb A 13 28 30
2YYG.pdb A 45 42 67
.
.
.
.
***PyMol Commands***
1) load 2YYI.pdb
2) hide everything
3) show cartoon
4) set cartoon_transparency, 0.8
5) set dash_gap, 0
6) set sphere_scale, 0.45
7) set sphere_mode, 4
8) bg_color white
9) select resi 13+28+30 and chain A and n. CA
10) distance d, sele and n. CA , sele and n. CA
11) hide labels, d*
12) show spheres, sele
13) color red, sele
14) save session_2YYI.pse
15) ray 1000,1000
16) png ~/Desktop/temp/2YYI_A.png
In the above set of commands, I am opening each PDB file as mentioned in the 1st
column of the input file, selecting chain as in the 2nd column, and selecting
residues as mentioned in the next 3 columns.
Also when i save the sessions and the png file, I am taking them from the input
file.
How can i automate this procedure such that I have a total of 2 png files and 2
sessions for each of the pdb that I am listing in the input file. I have tried
doing this but, cant get ahead due to errors.
I am not much of a coder in Python. PLease help.
This is how far i have got.
*****
from pymol import cmd
def process_line(x):
pdbid,res1,res2,res3 = x.split()
cmd.load(pdbid)
cmd.bg_color("white")
cmd.hide("everything")
cmd.show("cartoon")
cmd.select((resi %s + resi %s + resi %s and chain %s name
CA)"%(chain,res1,res2,res3))
cmd.distance("d","sele and n. CA, sele and n. CA")
cmd.hide("labels","d*")
cmd.color("sele", red)
cmd.show("spheres","sele")
cmd.ray(1000,1000)
cmd.save("%s_%s".pse)%(pdbid,chain)
cmd.png("%s_%s")%(pdbid,chain)
cmd.delete(pdbid.split(',')[0])
def process_all(filename):
for line in open(filename):
process_line(line)
process_all("testpy.txt")
*****
What is going wrong? how can this be automated for all the pdbid's listed in
input file ?
errors I get:
File "/usr/lib/pymodules/python2.6/pymol/parser.py", line 338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
File "/usr/lib/pymodules/python2.6/pymol/parsing.py", line 455, in run_file
execfile(file,global_ns,local_ns)
File "anu.py", line 19, in <module>
process_all("testpy.txt")
File "anu.py", line 17, in process_all
process_line(line)
File "anu.py", line 10, in process_line
cmd.save(thisSession.pse)
- Anasuya
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