[Chimera-users] Chimera - Saving multiple files

Elaine Meng meng at cgl.ucsf.edu
Sun Jun 19 09:13:49 PDT 2016


Hi Elza,

As I tried to describe before, you would NOT enter docking1.1.pdb.  You would enter:  docking$number.pdb

and choose (highlight with mouse) only those two models in the Models part of the dialog. That would give you two output files with names automatically including the numbers.

Elaine


On Jun 17, 2016, at 12:45 PM, Elza Sofia Fonseca <fonseca.ess at gmail.com> wrote:

> Hi Elaine,
> 
> Thank you for your help, but it didn't work...
> I want the protein - target.pdb (#0) - and the model (#1.1), so I selected these ones and in the name I wrote docking1.1.pdb and the error meaage appeared again...
> 
> 
> Best regards,
> 
> 
> 2016-06-16 18:02 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu>:
> 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:
> 
> docking$number.pdb
> 
> 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
> ----------
> 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.
> >
> 
> 
> 
> 
> -- 
> Elza Fonseca
> 
> 00351 966 199 802
>  
> PhD  student
> CIIMAR – AGE/EDEC 
> 
> http://www.ciimar.up.pt/researchgroup.php?id=AGE
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