[Chimera-users] Finding SASA for individual residues

[Prathvi Singh]

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 Thu, Nov 17, 2022 at 10:42 AM Prathvi Singh <prathvi at iitk.ac.in> wrote:

> Thank you so much Elaine!!
>
> On Mon, Nov 14, 2022 at 9:42 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> Hi Prathvi,
>> Yes, either one.
>>
>> 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>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> > On Nov 14, 2022, at 6:29 AM, Prathvi Singh via Chimera-users <
>> chimera-users at cgl.ucsf.edu> wrote:
>> >
>> > Hi Elaine,
>> > Can I use chimera or chimeraX to know the solvent accessible surface
>> area (SASA) for selected residues?
>>
>>
>
> --
> Prathvi Singh,
> Research Fellow,
> Department of Biological Sciences & Bioengineering,
> Indian Institute of Technology, Kanpur-208016
>


-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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