Hi Efrem,
do you still see the same behavior if you disable automatic change of colors
when loading your PDBs? The relevant setting would be auto_color set to off.
Does not quite answer your question, but could be a work-around.
HTH
Carsten
From: Efrem Braun [mailto:efrem.br...@gmail.com]
Sent: Friday, March 27, 2015 3:19 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] when number of atoms changes, colors change in an uncontrolled
manner
Hello,
I'm running a Monte Carlo simulations in which the number of atoms in my
simulation box changes over the course of the simulation. I print all atoms as
Hydrogen, so the colors of them should all be white. When I load the resulting
pdb file into PyMOL, the first frame has all atoms colored white, but by frame
3 some of the atoms have turned black, by frame 9 some atoms have turned orange
or blue, and by frame 15 lots of purple atoms show up (the purple atoms
disappear in frame 16 and reappear in frame 17 along with a whole bunch of
other colors).
I tried to troubleshoot this by typing "iterate all, print color." It printed
"29" for the 219 atoms it iterated over (at no frame does my simulation box
contain 219 atoms; the first 10 frames contain 200, 206, 209, 213, 206, 209,
221, 238, 235, and 253 atoms, and the last 10 all contain more than 253 atoms).
Since it doesn't appear to be iterating over all atoms, I suspect this
indicates what the problem is, but I can't figure it out.
I put frame 20 into its own pdb file and displayed it in pymol, and it
displayed all 428 atoms as white. So the problem definitely appears to be
coming from the fact that the number of atoms in the box is changing. With
simulations in which the number of atoms remains constant, I've never had this
problem.
This occurs both when I run on Linux (Version 1.7.0.0) or on a Mac (Version
1.7.2.1).
Any help would be greatly appreciated. Both pdb files are attached.
Efrem Braun
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