residue.areaSES returns 0 for buried residues
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
Hi Kevin, I think you are misunderstanding the the SES… it is not the complement of the SAS; the distinction is whether it is the surface traced out by the surface of the probe (SES) or the center of the probe (SAS) rolled over the structure of interest. SES is like a smoothed VDW surface of the molecule, since the crannies where the probe doesn’t fit are removed. Both SAS and SES will be zero for completely buried residues. I’m sure there are some good images showing the two types of surface, but I don’t have one handy at the moment. We have instructions for calculating the relative exposure of amino acid residues. It uses the SES of a residue in the structure of interest normalized by the SES of that same type of residue in an extended Gly-X-Gly tripeptide, as a proxy for the unfolded state: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html> If I remember correctly, the procedure gives fractional values, but they could be multiplied by 100 to give %. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 15, 2017, at 9:50 AM, Kevin Jude <kjude@stanford.edu> wrote:
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?
Elaine - Thanks, this is very helpful. I remember, now, calculating SES with GRASP years ago, but it's been a while, so I'd gotten my definitions confused. 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 On Fri, Sep 15, 2017 at 1:22 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Kevin, I think you are misunderstanding the the SES… it is not the complement of the SAS; the distinction is whether it is the surface traced out by the surface of the probe (SES) or the center of the probe (SAS) rolled over the structure of interest. SES is like a smoothed VDW surface of the molecule, since the crannies where the probe doesn’t fit are removed. Both SAS and SES will be zero for completely buried residues.
I’m sure there are some good images showing the two types of surface, but I don’t have one handy at the moment.
We have instructions for calculating the relative exposure of amino acid residues. It uses the SES of a residue in the structure of interest normalized by the SES of that same type of residue in an extended Gly-X-Gly tripeptide, as a proxy for the unfolded state: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html>
If I remember correctly, the procedure gives fractional values, but they could be multiplied by 100 to give %.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 15, 2017, at 9:50 AM, Kevin Jude <kjude@stanford.edu> wrote:
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?
participants (2)
-
Elaine Meng -
Kevin Jude