[Chimera-users] Question regarding saving PDB in Chimera

Pancera, Marie (NIH/VRC) [E] mpancera at mail.nih.gov
Tue Jan 6 06:29:28 PST 2009

Thanks, it definitively helps.
Finally I was able to save relative to the map and that was fine.

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Monday, January 05, 2009 5:29 PM
To: Pancera, Marie (NIH/VRC) [E]
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Question regarding saving PDB in Chimera

Hi Marie,
If you just want the transformed coordinates (as shown on the  
screen), don't check any options.  That is, don't use "save relative  
to" some model.  However, that only saves the atomic structure and  
not the map, so if you had rotated the entire view you would lose  
their relationship and the fitting.  I believe you want to save the  
atomic model relative to the density map model.

To save the original coordinates of a model, you would "save relative  
to" itself, for example, save model #0 relative to model #0.   
Normally that would be done if you did something like rotated a bond  
or added hydrogens but otherwise wanted the same coordinates as  
input.  Another use is if you superimposed or docked #0 and #1 and  
wanted to save their relative orientations.  In that case you could  
either save #1 relative to #0 (so that the saved #1 would work with  
the original file for #0) or vice versa, assuming both are atomic  

In your case, with a density map and an atomic structure, you can  
only save the atomic structure as PDB, of course.

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

On Jan 5, 2009, at 11:13 AM, Pancera, Marie (NIH/VRC) [E] wrote:
> Hello,
> I am using Chimera to fit coordinates into EM density.
> However I have problems when I save with Chimera as the coordinates  
> that I am saving are not the one I see on the screen.
> Here is what I do:
> File
> Save PDB
> chose the folder
> A file name
> A file type
> The model that I want to save, i.e the one I see on the screen
> And then I have to select save relative to model, otherwise I am  
> saving the original molecule, the problem is that I am not sure  
> relative to which model I have to save it.
> IS there an easier way to just save what I can see on the screen?
> Thanks,
> Marie

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