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 -- 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