Chimera-users October 2020

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bound ligand's are exposed to solvent. Current calculations do not protect surface of ligand embedded in protein
by Anne-Frances Miller 01 Oct '20

01 Oct '20

Dear Chimera, I see on-line advice on calculating areaSAS and areaSES, however Chimera is calculating these for my bound flavin as if the protein were not there. I would like to assess the area exposed outside the protein, not total area (on an atom-by-atom basis). Indeed, the show surface command produces two surfaces, one for the FAD and a different one for the protein, even though both are chain A. Can I edit the pdb file to cause Chimera to create a single surface for both chains including both bound FADs, so that SASA calculated will represent the extent to which the FAD protrudes from the protein? (My protein is a heterodimer with two bound FADs, my Chimera version is 1.13.1 running on Mac OS 10.15.6) Thank you, Anne-Frances Novel Meritorious Research (and teaching) —————————————— A.-F. Miller, Ph. D. Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin Chair, Div. of Biological Chemistry, American Chemical Society

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