[Chimera-users] residue.areaSES returns 0 for buried residues

Kevin Jude kjude at stanford.edu
Fri Sep 15 09:50:49 PDT 2017

Hi Chimerans-
I am trying to use Chimera to list percent accessible surface area by
residue for a structure by calculating (solvent accessible area SAS) /
(solvent excluded area, SES). For some reason, for residues that are
completely buried, Chimera returns not only SAS=0, but also SES=0, and thus
those residues aren't included in the percent accessible calculation. Does
anyone have a clue for this behavior?

My workflow is as follows:

File>Open  [choose pdb file]
> Actions>Surface>Show
> Tools>Surface/Binding Analysis>Measure Volume and Area
> Tools>Depiction>Render by Attribute
> in the render by attribute window:
> File>Save Attributes
> in the save window:
> select attribute 'areaSAS' or 'areaSES' of 'residues' and save to a file
> to calculate % accessible:
> Tools>Structure Analysis>Attribute Calculator
> in the attribute calculator window:
> Calculate attribute "percentaccessible" for "residues"
> Formula:
> (residue.areaSAS)/(residue.areaSAS+residue.areaSES)
> [check Save calculation results to file]

Best wishes

Kevin Jude, PhD
Research Specialist in Structural Biology, Garcia Lab
Departments of Molecular & Cellular Physiology and Structural Biology
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
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