[Chimera-users] write PDB from MDmovie

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 23 15:51:14 PDT 2019

Hi Victor,
Your file opens and looks like a normal protein in Chimera and ChimeraX.  I have no idea about Pymol, but there is something weird about the file: it has a whole bunch of extra CONECT lines at the end with integers larger than the atom numbers in the file. This is reported in the Log if you open the file in ChimeraX.   I don’t know what trajectory format you had, or whether you deleted a whole bunch of atoms like all the waters, but probably if you just remove the CONECT lines at the bottom of this PDB file with a text-editor or script, it may behave normally in Pymol too.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 23, 2019, at 3:21 PM, Kenyon, Victor <vkenyon at coh.org> wrote:
> Hi All,
> When writing a PDB from a frame of MDmovie I get something that looks a little more like a Picasso than a protein (see attached image, if available).
> I am assuming I am doing something incorrect, however, all of the documentation I see online points to the same way of writing a file.
> If anyone has experience with this issue, please let me know if there is a resolution. I have included the coordinates —with waters and ions removed— below from the output.
> Thanks!
> victor

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