[Chimera-users] Serine 371 in a protein (ATR)

[Elaine Meng]

Hi Leif,
This is more a “scientific advice” question than about Chimera per se (what this mailing list is supposed to cover), but I don’t see why not, if the numbering in your structure matches with whatever information source told you about that interaction.  It won’t give you the orientations of the proteins, of course, just a ballpark idea. 

Not sure what you mean by “PDBQT image” … PDB and PDBQT have atomic coordinates, in which you could find specific atoms or residues.  If you are showing the molecular surface, like for electrostatic coloring, you may need to hide it at least temporarily (e.g. un-check the “S”hown button in the Model Panel) to find the find the residue in the atomic structure. 

You could select the residue to highlight it in green, such as in the Sequence (show with Favorites… Sequence) or a command (e.g. “select :371”).
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 22, 2019, at 4:07 PM, <leifepeterson at sbcglobal.net> <leifepeterson at sbcglobal.net> wrote:
> 
> Hi Elaine,
>  
> A particular protein binds with e.g. Serine-371 of another protein (ATR).  In order to find that pocket in a PDBQT image of ATR, can I simply look for AA=371?
>  
> Thanks,
>  
> Leif Peterson