[chimerax-users] Finding Continuous Residue Stretches

[Elaine Meng]

Dear Dan,
In ChimeraX, you can calculate solvent-accessible surface area (SASA) per residue and write out those values to a text file (a file containing values of the "area" residue attribute) , but you would need to postprocess the file yourself to identify consecutive stretches of residues with sufficient SASA to qualify as being on the surface in your opinion.

Or, you could select based on some SASA cutoff and only include those residues in the file, if that helps, as in the example below:

Example commands

open 3u82
measure sasa protein
select ::area>50
save ~/Desktop/residue-areas.defattr attrName r:area selectedOnly true

The text file contents look like this:

attribute: area
recipient: residues
match mode: 1-to-1
        /A:23   99.25012396893807
        /A:24   151.03479779520194
        /A:25   80.3897831024973
        /A:26   119.86834409282129
[... etc. ...]

The example selects only residues with >50 square angstroms SASA but you could change it to whatever you feel is appropriate, or skip selecting and just save all the values for all residues to the file.  I'm on a mac and can save to my Desktop but you could change output file pathname as appropriate for your system and the filename you want, except keeping the suffix ".defattr"

See help for details: 
measure sasa
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>
saving attribute values to file
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>
attribute file format
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>

Bear in mind that when ChimeraX displays a surface, it is the solvent-excluded surface (SES) not the SAS.  The difference is illustrated here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> 

Instead of writing a file and postprocessing completely separate from ChimeraX, you could probably do it with python code input to ChimeraX, but that is beyond my expertise (and might be complicated).

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 23, 2021, at 3:06 PM, Daniel Wells via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimerax Users:
> 
> I need to find Continuous Residue Stretches between 15-25 amino acids in length on the surface of these two molecules:
> 
> https://www.rcsb.org/3d-view/4MYV/1
> 
> https://www.rcsb.org/structure/3U82
> 
> Could anyone here help me perform that function on Chimerax? 
> 
> Thank you for your time.
> 
> Sincerely,
> 
> Dan Wells