Hello, Is there any way to select/color all protein residues with incomplete sidechains? This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site). Cheers, Oliver.
Hi Oliver, Attached is a script that Eric made me years ago to select all the incomplete residues. I just did a spot-check on 5BTR and opening this script did select all the residues with missing atoms that were listed in the PDB header. 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 P.S. I don’t see it listed in this Chimera Python-scripts page, will add it soon… <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
On Jan 19, 2016, at 1:59 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hello,
Is there any way to select/color all protein residues with incomplete sidechains?
This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site).
Cheers, Oliver. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Elaine! That looks like it'll do the trick nicely :) Oli. On Tue, Jan 19, 2016 at 5:20 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, Attached is a script that Eric made me years ago to select all the incomplete residues. I just did a spot-check on 5BTR and opening this script did select all the residues with missing atoms that were listed in the PDB header.
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
P.S. I don’t see it listed in this Chimera Python-scripts page, will add it soon…
<http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
On Jan 19, 2016, at 1:59 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hello,
Is there any way to select/color all protein residues with incomplete sidechains?
This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site).
Cheers, Oliver. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Oliver Clarke