[Chimera-users] [chimera-dev] Trouble with Saving New Atom Attributes

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 5 14:54:57 PDT 2013


Hi Juliette,
PDB format does not include atom-type information, as you have seen.  The only sure way to save your atom type changes is to save the Chimera session.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html>

However: 
Chimera applies chemical perception to try to figure out the atom types when a structure is read in from a file. The Mol2 format does have some atom-type information, but the SYBYL Mol2 types are not related 1-to-1 to the types in Chimera.  You could try saving in Mol2 format and reading it back in to see if the information you want is retained.  Further, if you have added all hydrogens before writing the file (PDB or Mol2) the chemical perception is more well-determined and it is possible that it will assign the types you intended.  If those do not work, however, the session is the way to go.

If you just wanted a list of the assignments rather than the assignments per se, you could use  "File... Save Attributes" from the menu of Render by Attribute (itself in menu under Tools... Depiction).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

This seems more like a "user" question than a developer (programmer) one; it's not necessary to email both lists.  
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 Jul 5, 2013, at 2:34 PM, Juliette Cao wrote:

> Hi All,
> I was successfully able to change a few atom types using the setattr command.
> I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.)
> I saved the .pdb file
> When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. 
> Is there a specific way to save files after using setattr command?
> Regards,
> Juliette Cao
> University of Houston




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