Hi Efrem,
your PDB file doesn't have any atomic identifiers, except the "ID" column. The
atom "ID" is not used to match atoms when loading multiple models, but
basically all other atomic identifiers are (segi, chain, resi, resn, name). So
if you assign for example a unique residue number (resi) to every atom, your
file should load correct.
You can copy the ID column to the resi column in your PDB file with this Python
program:
import sys
for line in open('test.pdb'):
if line.startswith('ATOM '):
line = line[:22] + line[7:11] + line[26:]
sys.stdout.write(line)
Hope that helps.
Cheers,
Thomas
On 30 Mar 2015, at 14:15, Efrem Braun <efrem.br...@gmail.com> wrote:
> Carsten,
>
> Yes, the same behavior results. I did:
> set auto_color, off
> load test.pdb
> set auto_color, off
>
> And the colors remained. (I set auto_color to off twice just to be sure).
>
> Efrem Braun
>
> On Mon, Mar 30, 2015 at 11:04 AM, Schubert, Carsten [JRDUS]
> <cschu...@its.jnj.com> wrote:
> 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
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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