Hi Antonio,
I got the same error message after the second line but this worked for me.
/Applications/PyMOL.app/Contents/bin/python
>>>from pymol import cmd
>>>fcmd.fetch("5da6")
>>>fcmd.do("show sticks; hide cartoon;orient")
>>>fcmd.util.cbac('all')
>>>fcmd.png("testcbacSticks.png")
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: Antonio Serrano [aserra...@ucam.edu]
Sent: Monday, September 14, 2020 10:57 AM
To: pymol mailinglist
Subject: [EXTERNAL] [PyMOL] Color by Atom from CLI (not PyMol's GUI)
Hi. I'm working with PyMol's Python API from the terminal. I would like to
color the molecules in my session by atom using the command util.cbac(). I want
them in cyan because I'm deleting the two molecules involved and reopening the
files with those molecules several times inside a loop. My first attempt was
this:
import pymol2
sess = pymol2.PyMOL()
sess.start()
sess.cmd.load("./cyclodextrin_rec.mol2", object = "rec")
sess.cmd.load("./cyclodextrin_lig.mol2", object = "lig")
sess.cmd.util.cbac("all")
After that last command, I get the following warning message: "PyMOL not
running, entering library mode (experimental)". It is supposed to work, but I
don't get the molecules colored by atom. I also tried with the following last
command instead of sess.cmd.util.cbac("all"):
import pymol
pymol.util.cbac("all")
But still doesn't work. Any clue? Thx.
Antonio Serrano
[http://ucam.edu/logo-firma-electronica.png]
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