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

[Prathvi Singh]

You guessed it right. I missed the "e" part.
Thanks again!

On Wed, Mar 1, 2023 at 10:01 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> >
>
>

-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230302/22e1cc68/attachment.html>