[Chimera-users] select atoms near at least one other atom in original selection?

Oliver Clarke olibclarke at gmail.com
Tue Nov 1 11:11:38 PDT 2016


Hi Elaine - close but not exactly. I’d like to select any residue in the current selection that is near at least one other residue which is also within the current selection - does that make sense? The idea is to identify spatial clusters within the selected residues. Maybe i’ll need to script to do this?

Oli
> On Nov 1, 2016, at 2:04 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Oli,
> To select all residues with any atom within 10 angstroms of current selection:
> 
> sel sel zr<10
> 
> I wasn’t totally sure if that was what you wanted. If you just want atoms and not whole residues, it would be za instead of zr.
> Best,
> 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 Nov 1, 2016, at 10:47 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>> Hi,
>> 
>> I’d basically like to perform the equivalent of “hide dust” on an atom selection. I have a bunch of mutation positions that I’ve mapped onto a structure, and I would like to create a subselection containing only those positions which are within lets say 10Å of at least one other postion in the original selection - basically to represent  structural clusters of mutations on the structure. Does anyone have any suggestion how to create such a selection using Chimera’s atom selection language? It seems like zr should do it but I can’t quite figure out how.
>> 
>> Cheers
>> Oli.
> 




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