Discrepancies in SASA values between chimera and chimeraX
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.
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@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.
You guessed it right. I missed the "e" part. Thanks again!
On Wed, Mar 1, 2023 at 10:01 PM Elaine Meng meng@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 120.25633132457733Compare 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@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.
participants (2)
-
Elaine Meng -
Prathvi Singh