[chimerax-users] Discrepancies in SASA values between chimera and chimeraX

[Elaine Meng]

Hi Prathvi,
Actually all of the values are the same between Chimera and ChimeraX, up to a few digits after the decimal due to small rounding differences.  The ones you are looking at are exponentially small and would round to zero -- you probably just didn't see the "e" part of the number.

For example, residues 10-20 from Chimera (including your example residue 18):

        :10.A   75.444729387760162
        :11.A   60.271224021911621
        :12.A   78.07588455080986
        :13.A   98.425362586975098
        :14.A   0.048496511066332459
        :15.A   36.617062151432037
        :16.A   71.055649171234109
        :17.A   58.565219432115555
        :18.A   0.0
        :19.A   98.871001124382019
        :20.A   120.25633132457733

Compare to values for residues 10-20 from ChimeraX:

residue id /A:10 area 75.44474043673931 index 9
residue id /A:11 area 60.27123586914773 index 10
residue id /A:12 area 78.07587694199468 index 11
residue id /A:13 area 98.42534378238655 index 12
residue id /A:14 area 0.048495996331269 index 13
residue id /A:15 area 36.617058903269864 index 14
residue id /A:16 area 71.05562083968395 index 15
residue id /A:17 area 58.56521161974685 index 16
residue id /A:18 area -2.842170943040401e-14 index 17
residue id /A:19 area 98.87095424593323 index 18
residue id /A:20 area 120.25635353116752 index 19

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

> On Feb 28, 2023, at 11:10 PM, Prathvi Singh via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> I compared the SASA values generated by chimera and chimeraX for a few PDB files and I noticed that whenever the SASA value of a residue is reported to be zero by chimera, the same residue's SASA value is reported to be -1.42 by chimeraX. Few examples are 18.A and 38.A of the PDB ID 1A62.
> 
> Method used to calculate SASA of residues in chimera: Tools > Structure analysis > Render by attribute
> Method used to calculate SASA of residues in chimeraX: I ran the following commands: measure sasa protein;info residues attribute area
> 
> Why is this happening? Kindly help.
>