[Chimera-users] bound ligand's are exposed to solvent. Current calculations do not protect surface of ligand embedded in protein

[Anne-Frances Miller]

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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