[chimerax-users] identifying surface residues

[Elaine Meng]

On Aug 23, 2021, at 2:54 PM, Brian Yang <by2289 at columbia.edu> wrote:
> 
> Dear Dr. Meng,
> I hope you are doing well. My name is Brian. I am a senior at Columbia University. I am currently doing research at the Columbia University Medical Center. I am contacting you because I have a few questions about using Chimera X.
> 
> I am trying to use Chimera X to identify surface residues on a protein. [...]
> 
> I have been looking through the Chimera API, and I found this method that I think could work:
> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html
> 
> However, I'm not able to figure out how to do the Attribute Calculator in Chimera X, nor am I able to get the SES area.
> 
> I saw your response in this email chain:
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-September/001484.html
> 
> and I have tried it, but this is only for SAS area.
> 
> So my questions are: 
> Do you think the surfnorm method is appropriate? If so, how would I achieve the Attribute Calculator functionality in Chimera X? If not, could you give me a better approach to remove these surface residues?
> 
> Thank you for your time!
> 
> Kind regards,
> Brian Yang
> 

Hi Brian!
For asking questions about ChimeraX, we recommend using the  address chimerax-users at cgl.ucsf.edu (CC'd here so you don't need to do anything this time) unless you are including something that needs to remain private.  I edited out some details about your project above just in case.

ChimeraX does not calculate solvent-excluded surface area (SESA) nor does it have an Attribute Calculator tool.  However, if all you want to do is to identify which residues are on the surface, you could:

(1) calculate solvent-accessible surface area (SASA) per residue.  Command "measure sasa protein setAttribute true" or something like that.  The "protein" part is that so waters, ligands, etc. are not enclosed in the calculated surface.  The "setAttribute true" part assigns values to a residue attribute named "area" so that you can do the next step, although it could be omitted since it is already true by default. There are various other options too. 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>

(2) delete all residues with SASA greater than some value.  You wouldn't be normalizing to a percentage exposed since we don't have the values to use for the denominator, but just the raw amount of solvent-accessible area.  So you may want to tinker around with what value of the cutoff gives you reasonable results.  
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes>

Example:

open 4hvp
measure sasa protein setAttribute true
show 
hide ~protein
hide ribbons
sel ::area>20
color sel red
color ~sel white
~sel

... see what you think, or try some other value...

sel ::area>15
color sel red
color ~sel white
~sel

When you figure out what value you want to use, you could delete those residues, e.g.

delete ::area>15

...or if you're not sure what to use as a single cutoff and may want to process several times at different cutoffs, you can just write out all of the residues and their area values to an "attribute file"... see
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>

However, if you really need a % exposure value normalized to account for different residue sizes, you would need to stick with Chimera, at least for now.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco