[chimerax-users] [Chimera-users] Finding SASA for individual residues

[Elaine Meng]

On Nov 17, 2022, at 8:01 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> The methods you suggested for calculating SASA for residues saved me so much time. Thank you once again for it.
> But I have noticed an ambiguity.
> When I calculate the SASA for the same residue using chimera and chimeraX, I am getting different values.
> For ex: in the PDB file 1TY4, the SASA value  for residue 174.a is 2.55 when calculated using chimera and it is 292.44 when calculated using chimeraX. The same is true for other amino acids in other PDB files as well.
> Why is there such a difference?
> On which of the two software should I rely on?
> Also, what is the unit of SASA calculated by these two softwares?
> 
> On Mon, Nov 14, 2022 at 9:42 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> [...]
> In Chimera, they are automatically calculated when you show a molecular surface.  It creates an attribute named areaSAS, as explained here:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>
> 
> See also this previous chimera-user post on using Chimera to get a list of residue SASA values
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2018-June/014729.html>
> 
> (If you use this page <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> to search chimera-users by "sasa", that was the top hit)
> 
> In ChimeraX, you would use the command "measure sasa" 
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>
> ... then save attribute "area" to file
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>
> 

Hi Prathvi,
The atomic coordinates are in angstroms so the surface areas are in angstroms squared. Since this answer is mostly about ChimeraX, I'm also CCing the chimerax-users list.

Regarding the differences in value:
The programs are both right but based on different surfaces.  By default, Chimera encloses all of the protein chains together into one surface (and chain A residue 174 is buried by some interactions with chain C, which you can probably see if you look at the structure). In ChimeraX, the default for display is to make each chain a separate surface, but for SASA calculation, it only depends on what you wrote in the "measure sasa" command.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>

As mentioned in my earlier answer, the important part of what you get from "measure sasa" is not (in your case) the total reported in the Log, but instead the "area" attribute value that you will get for each residue.

If you just use this ChimeraX command:

measure sasa /A:174 

... then it will make a surface that only encloses that one residue, with area 292 as you said.  I'm pretty sure that is NOT what you want.  Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. 

If you wanted to enclose all the protein chains of a model in a single surface (like Chimera default), then

measure sasa protein

 If you wanted to make a separate surface for chain A only, then something like

measure sasa /A & protein 

(the & protein part is still needed so that it won't enclose ligands, water, etc. that also happen to have chain ID A)

Using "measure sasa" gives the residue "area" attribute that you could save to file, show in labels, etc. as explained in the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>
<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html>

For your example structure 1TY4, using these ChimeraX commands:

measure sasa protein
info residues attribute area

...gives 2.55 for residue 174 in chain A, the same as in Chimera.

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