<div dir="ltr"><div>Hi Chimerans-<br></div>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?<br><br>My workflow is as follows:<br><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">File>Open [choose pdb file]<br>Actions>Surface>Show<br>Tools>Surface/Binding Analysis>Measure Volume and Area<br>Tools>Depiction>Render by Attribute<br><br><div>in the render by attribute window:<br></div><div>File>Save Attributes<br><br></div><div>in the save window:<br></div><div>select attribute 'areaSAS' or 'areaSES' of 'residues' and save to a file<br></div><div><br></div>to calculate % accessible:<br>Tools>Structure Analysis>Attribute Calculator<br><br>in the attribute calculator window:<br>Calculate attribute "percentaccessible" for "residues"<br>Formula:<br>(residue.areaSAS)/(residue.<wbr>areaSAS+residue.areaSES)<br>[check Save calculation results to file]</blockquote><div><br></div><div>Best wishes</div><div>Kevin<br></div><div> <br></div><div><div><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><span><div>--<br></div><div>Kevin Jude, PhD<br>Research Specialist in Structural Biology, Garcia Lab</div><div>Departments of Molecular & Cellular Physiology and Structural Biology</div><div>Stanford University School of Medicine</div><div>Beckman B177, 279 Campus Drive, Stanford CA 94305</div><div>Phone: <a href="tel:%28650%29%20723-6431" value="+16507236431" target="_blank">(650) 723-6431</a></div></span></div></div></div></div></div></div></div>
<div dir="ltr"><br></div></div></div></div>