That works! Thanks!
Efrem Braun
On Wed, Apr 8, 2015 at 1:49 PM, Thomas Holder <thomas.hol...@schrodinger.com
> wrote:
> 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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