select atoms near at least one other atom in original selection?
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.
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@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.
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@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@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.
Hi Oli, I was going to say “not with commands” but then I thought of a way… it is somewhat circuitous, however, so you might prefer to script a more direct route. My idea is to use findclash to identify inter-residue “contacts” where a contact is defined as VDW surfaces of atoms within X angstroms, select those pairs of atoms, and then (if you want) promote the selection of atoms to whole residues. The subtlety is that you have to define your desired cutoff in terms of separation of VDW surfaces rather than atomic center-center distance. So for VDW surfaces within 3 angstroms, findclash sel test self overlap -3 hb 0 intraRes false select true sel up Maybe that will suffice… Elaine
On Nov 1, 2016, at 11:11 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
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@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@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.
Yeah, Elaine’s idea is fiendishly clever. The basic problem in using “zone” is that a zone can’t exclude the atoms it’s based on, so you always wind up selecting all the original atoms. There is a Python script named “selLys.py” on the Scripts page of the Chimera wiki (http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>) that selects lysine residues within 8 angstroms of another lysine residue. You could easily adapt that script to your problem. Or you could do the findclash thing. :-) —Eric
On Nov 1, 2016, at 1:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, I was going to say “not with commands” but then I thought of a way… it is somewhat circuitous, however, so you might prefer to script a more direct route.
My idea is to use findclash to identify inter-residue “contacts” where a contact is defined as VDW surfaces of atoms within X angstroms, select those pairs of atoms, and then (if you want) promote the selection of atoms to whole residues. The subtlety is that you have to define your desired cutoff in terms of separation of VDW surfaces rather than atomic center-center distance. So for VDW surfaces within 3 angstroms,
findclash sel test self overlap -3 hb 0 intraRes false select true sel up
Maybe that will suffice… Elaine
On Nov 1, 2016, at 11:11 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
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@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@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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Thanks Eric, thanks Elaine - haven’t tried the script yet but Elaine’s find clash trick did exactly what I was after, very clever indeed! Cheers Oli
On Nov 1, 2016, at 4:15 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Yeah, Elaine’s idea is fiendishly clever.
The basic problem in using “zone” is that a zone can’t exclude the atoms it’s based on, so you always wind up selecting all the original atoms. There is a Python script named “selLys.py” on the Scripts page of the Chimera wiki (http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>) that selects lysine residues within 8 angstroms of another lysine residue. You could easily adapt that script to your problem.
Or you could do the findclash thing. :-)
—Eric
On Nov 1, 2016, at 1:00 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi Oli, I was going to say “not with commands” but then I thought of a way… it is somewhat circuitous, however, so you might prefer to script a more direct route.
My idea is to use findclash to identify inter-residue “contacts” where a contact is defined as VDW surfaces of atoms within X angstroms, select those pairs of atoms, and then (if you want) promote the selection of atoms to whole residues. The subtlety is that you have to define your desired cutoff in terms of separation of VDW surfaces rather than atomic center-center distance. So for VDW surfaces within 3 angstroms,
findclash sel test self overlap -3 hb 0 intraRes false select true sel up
Maybe that will suffice… Elaine
On Nov 1, 2016, at 11:11 AM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
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@cgl.ucsf.edu <mailto:meng@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@gmail.com <mailto:olibclarke@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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participants (3)
-
Elaine Meng -
Eric Pettersen -
Oliver Clarke