[Chimera-users] Chimera help submission

Tom Goddard goddard at sonic.net
Thu Feb 25 09:54:30 PST 2021

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 <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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