[Chimera-users] Saving PDBs

Elliott, Jabari jielliott at wustl.edu
Wed Oct 17 14:47:09 PDT 2018


I believe that the “selection” option is the issue. 

Thank you 

> On Oct 17, 2018, at 16:44, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hello,
> I do not have this problem when saving multiple models to a single PDB file.  When I reopen the saved file in Chimera, the atoms/models are all present.  All I can say is that in the PDB-saving dialog, make sure you haven’t turned on (checked) the options “Save displayed atoms only” or “Save selected atoms only” because if you don’t have displayed atoms or selected atoms, respectively, then your file will contain zero atoms.
> In Chimera “selection” means specifically highlighted in the structure with green outlines, like when you Ctrl-click on some atom.  It does not mean the models you chose (highlighted) in the PDB-saving dialog.
> Saving PDB files:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Oct 17, 2018, at 2:11 PM, Elliott, Jabari <jielliott at wustl.edu> wrote:
>> When attempting to save PDBs of multiple models into one file, I end up with a pdb file with no data (0-600 bytes). When attempting to open files in pymol, they are blank. Please advise. Thank you.

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