Identify hinges and rigid groups using Morph Conformations?
Hi,
I gather from reading the documentation for “Morph Conformations” (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html) that Chimera identifies hinge regions and rigid groups as part of the procedure (as per http://nar.oxfordjournals.org/content/28/8/1665.long).
Would it be possible to expose these to the user (or maybe this is already possible?), such that one can color/label the hinges and rigid entities as desired? This would be helpful for visual simplification of complex conformational changes.
Cheers, Oliver.
Hi Oliver,
This could be done. Maybe the atoms of each region identified by the morph algorithm could be assigned an attribute like “morph_group” which would be an integer. It wouldn’t be too convenient to use these but you can specify sets of atoms with a specific attribute value. Maybe the morph command itself could be given an option to color each group. In any case, this would only be done in ChimeraX, not Chimera, and we don’t have morphing in ChimeraX yet. I’ve put a feature request in our ChimeraX database for this.
Tom
On Dec 18, 2015, at 1:06 PM, Oliver Clarke wrote:
Hi,
I gather from reading the documentation for “Morph Conformations” (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html) that Chimera identifies hinge regions and rigid groups as part of the procedure (as per http://nar.oxfordjournals.org/content/28/8/1665.long).
Would it be possible to expose these to the user (or maybe this is already possible?), such that one can color/label the hinges and rigid entities as desired? This would be helpful for visual simplification of complex conformational changes.
Cheers, Oliver. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Unfortunately, this is not a simple task. There are actually several layers of heuristics beyond the referenced procedures, mainly to handle small segments and chain identifiers, so the results may not be as clean as one would expect. Also, we would then have to come up with some sort of naming/attribute scheme so that different parts can be referenced. This may fall more in the ChimeraX realm at this point. Sorry.
Conrad
On 12/18/2015 1:06 PM, Oliver Clarke wrote:
Hi,
I gather from reading the documentation for “Morph Conformations” (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html) that Chimera identifies hinge regions and rigid groups as part of the procedure (as per http://nar.oxfordjournals.org/content/28/8/1665.long).
Would it be possible to expose these to the user (or maybe this is already possible?), such that one can color/label the hinges and rigid entities as desired? This would be helpful for visual simplification of complex conformational changes.
Cheers, Oliver. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Makes sense, thanks for checking it out.
Cheers, Oliver.
On Mon, Jan 4, 2016 at 3:14 PM, Conrad Huang conrad@cgl.ucsf.edu wrote:
Unfortunately, this is not a simple task. There are actually several layers of heuristics beyond the referenced procedures, mainly to handle small segments and chain identifiers, so the results may not be as clean as one would expect. Also, we would then have to come up with some sort of naming/attribute scheme so that different parts can be referenced. This may fall more in the ChimeraX realm at this point. Sorry.
Conrad
On 12/18/2015 1:06 PM, Oliver Clarke wrote:
Hi,
I gather from reading the documentation for “Morph Conformations” ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html ) that Chimera identifies hinge regions and rigid groups as part of the procedure (as per http://nar.oxfordjournals.org/content/28/8/1665.long).
Would it be possible to expose these to the user (or maybe this is already possible?), such that one can color/label the hinges and rigid entities as desired? This would be helpful for visual simplification of complex conformational changes.
Cheers, Oliver. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Conrad Huang -
Oliver Clarke -
Tom Goddard