[chimerax-users] [Chimera-users] calculating % exposed surface area

[Tom Goddard]

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 at 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 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
>> 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 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: 
>>> <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
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