[Chimera-users] calculating % exposed surface area
meng at cgl.ucsf.edu
Thu Feb 25 10:40:23 PST 2021
Currently it is not possible to use ChimeraX for this specific workflow, however, because it does not calculate residue solvent-excluded surface (SES) area values. The values supplied for normalization in that page (to calculate % exposed) are SES calculated with the Chimera parameters. These were kindly supplied by another group, as cited in that page.
The ChimeraX command "measure sasa" measures solvent-accessible surface (SAS) area and can assign the per-residue and per-atom values as attributes.
Theoretically somebody could generate the GXG tripeptides as proxy for the fully exposed state and measure SAS for each X in ChimeraX to compile a list of suitable values for normalization to calculate % exposed, but as far as I know, it hasn't been done.
Here's diagram showing the difference between SES and SAS for those who may not be familiar with these terms:
> On Feb 25, 2021, at 9:54 AM, Tom Goddard <goddard at sonic.net> wrote:
> Hi David,
> Maybe your structure has ligands, ions, or solvent atoms -- no surface is computed for those and so they don't get an areaSES attribute. You could put in a check
> if hasattr(r, 'areaSES'):
> r.relSESA = r.areaSES/ r.areaSESgxg
> print 'Residue has no areaSES', r, 'type', r.type
> You might be interested instead using our newer program ChimeraX. Chimera often fails to compute molecular surfaces and SES areas for large structures. ChimeraX uses new code that always works.
>> On Feb 25, 2021, at 5:53 AM, David Leeming <david.leeming at student.manchester.ac.uk> wrote:
>> Dear Chimera users,
>> I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html
>> The script I have is as follows:
>> rc('surface') # defines areaSES of residues
>> rc('defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0') # define attribute using areaSESgxg.txt
>> for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
>> for r in m.residues:
>> r.relSESA = r.areaSES/ r.areaSESgxg
>> However, when I run this script, I am receiving this error:
>> When I run the process using the UI I can successfully calculate relSESA
>> By using the command: "surface"
>> Then using the assign attribute function to assign areaSESgxg.txt
>> Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg
>> Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI.
>> Kind regards,
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
More information about the Chimera-users