Hi Elaine,

Good point. Forgot ChimeraX computes SAS area and not SES area. It makes more sense from a science perspective to use SAS I think -- the functionally relevant quantity is how much room there is for a ligand to be in contact and I think SAS will better reflect that than SES, although the correlation is no doubt very high between SES and SAS areas.

Tom

On Feb 25, 2021, at 10:40 AM, Elaine Meng meng@cgl.ucsf.edu wrote:

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. <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html >

The ChimeraX command "measure sasa" measures solvent-accessible surface (SAS) area and can assign the per-residue and per-atom values as attributes. https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa

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: https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#surfdefs

Elaine

...

On Feb 25, 2021, at 9:54 AM, Tom Goddard goddard@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 else: 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.

Tom

...

On Feb 25, 2021, at 5:53 AM, David Leeming david.leeming@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: <Outlook-1he3xhiv.png> 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, David _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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