Hi Hrutvik,
After run script.py, enter 'load filenane' to run the function.
Your function load() only prints the PyMOL commands that you want to execute.
Add below or above the print lines, add these indented lines.
cmd.do("load 1u8q.pdb")
cmd.do("color red, (chain y)" )
You might consider splitting the load and color into two separate functions to
make your code easier to read and use.
Functions in Python are suppose to do only one thing.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Hrutvik Bhavsar [hrutvi...@gmail.com]
Sent: Wednesday, July 01, 2020 6:26 PM
To: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] [PyMOL] Question about python commands in PyMOL
Hello,
I'm writing a python script that loads in PDBs then selects certain chains
colors them according to a standardized chart. However, I've run into the issue
where my when I try running my script in Pymol via the run command it just
displays the text on the python script but doesn't actually execute the
command. I've pasted a sample script below. Please let me if there's a way to
fix this. Thank you for your help.
Sincerely, Hrutvik.
from pymol import cmd, stored
def load( arg1):
print ("load 1u8q.pdb")
print ("color red, (chain y)" + "\n")
return (arg1)
cmd.extend( "load", load );
cmd.extend( "color", color );
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