[Chimera-users] Chimera - Saving multiple files

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 16 10:02:10 PDT 2016

Hi Elza,
This is not a bug, just a question (so it should go to the chimera-users email address only, not chimera-bugs).

Literally, you must enter a name that includes either “$name” or “$number” into the output-filename area.  Then that part will be replaced by the model name or model number of the individual docking, to create multiple different output filenames.  You can’t just enter a name without one of those because multiple names are required for multiple output files, not a single name. 

You can see the model names and model numbers of the docking results in the “Save models” area of the PDB-saving dialog (Chimera menu: File… Save PDB).

For example, if you enter File name in the PDB-saving dialog as:


It will write model #1.1 to a file named docking1.1.pdb, model #1.2 to a file named docking1.2.pdb, etc.  

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 16, 2016, at 3:48 AM, Elza Sofia Fonseca <fonseca.ess at gmail.com> wrote:
> Dear all,
> I am Elza Fonseca, a PhD student of the University of Porto and I am now learning to do dockings.
> I am using Chimera for open the results from SwissDock and I would like to save it like a multiple file. However I always get the same error message:
> "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". I don't understand what "$name or $number" means...
> May you please help me solving it? I apologize for my ignorance.

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