[Chimera-users] Overlay binding sites

Markus Heller mheller at cdrd.ca
Thu Nov 28 12:09:28 PST 2013


Hello all,

I'm pretty sure this has been done before, so before re-inventing the wheel or failing miserably and doing everything by hand, I thought I'd ask here first :)

I have a protein that has been crystallized with about a dozen ligands of different sizes.  I'd like to overlap the protein residues forming the binding site.  My plan was to pick the 2 largest ligands, select all protein residues within say 7 A, and consider these to be the residues forming the binding site.

Then, I'd like to match this set of residues for all proteins to the same reference.

I suppose I could do this all manually, but I'm hoping that there is a quicker, more efficient way!

Any tips are appreciated!

Thanks and Cheers
Markus
--
Markus Heller, Ph.D.
NMR Scientist
CDRD - The Centre for Drug Research and Development
2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147
Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller at cdrd.ca<mailto:mheller at cdrd.ca> | www.cdrd.ca
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