Finding SASA for individual residues
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
Hi Elaine, I'll reply to this post for my question cause the title seems appropriate. I've a one-chain protein and I simply want to calculate the SASA of the aromatic-ring of all TRP,TYR and PHE of the protein using ChimeraX. This is the log: measure sasa /A Solvent accessible area for /A = 22276 measure sasa /A:trp & aromatic-ring Solvent accessible area for /A:trp & aromatic-ring = 1824.9 measure sasa /A:phe & aromatic-ring Solvent accessible area for /A:phe & aromatic-ring = 3339.6 measure sasa /A:tyr & aromatic-ring Solvent accessible area for /A:tyr & aromatic-ring = 3977.3 But the I tried to get the sum: measure sasa /A:trp,tyr,phe & aromatic-ring sum :trp,tyr,phe Solvent accessible area for /A:trp,tyr,phe & aromatic-ring = 7683.3 Solvent accessible area for :trp,tyr,phe (285 atoms) of /A:trp,tyr,phe & aromatic-ring = 7683.3 Which is different from the sum of the values I got before. I think I'm missing something basic on SASA calculations... Also, from your answer to Prathvi, those numbers should be squared Agstrom. Do these number make sense? For a single residue (measure sasa:263, which is a surface-exposed Tyrosine) I got 331.95. Those values are similar to what Prathvi got so am I doing the same mistake? I was expecting, for a single residue something like two order of magnitude less. You said ".. 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. " Does this means that with the commands I typed ChimeraX "Isolates" the residue and calculate the SASA as if it was not included in the protein? Anyway, I think it is clear I'm an unexpert user so If there is any tutorial about SASA on ChimeraX (could not find those, only for Chimera), please, feel free to suggest. Thank you!! Best, Ale
Hi Ale, In the future please use chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) for ChimeraX questions. This chimera-users@cgl address is for Chimera, which is a different program, and I don't want to confuse the other users. Everybody, this answer is for ChimeraX: I believe you are misunderstanding how "measure sasa" works. It will actually enclose the specified atoms in a surface, so if you say "measure sasa :12" that surface will only be around residue 12 and ignore all the other atoms. I am guessing that you really want the SASA of the aromatic rings in the context of the surface that goes around the whole protein, not for a bunch of individual bubbles drawn around each aromatic ring. In that case, your commands are wrong. Instead you want something like: measure sasa protein sum :trp,tyr,phe & aromatic-ring See "measure sasa" help for description of how it works: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 29, 2024, at 4:16 AM, alessandro.strofaldi--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I'll reply to this post for my question cause the title seems appropriate. I've a one-chain protein and I simply want to calculate the SASA of the aromatic-ring of all TRP,TYR and PHE of the protein using ChimeraX.
This is the log: measure sasa /A Solvent accessible area for /A = 22276 measure sasa /A:trp & aromatic-ring Solvent accessible area for /A:trp & aromatic-ring = 1824.9 measure sasa /A:phe & aromatic-ring Solvent accessible area for /A:phe & aromatic-ring = 3339.6 measure sasa /A:tyr & aromatic-ring Solvent accessible area for /A:tyr & aromatic-ring = 3977.3
But the I tried to get the sum:
measure sasa /A:trp,tyr,phe & aromatic-ring sum :trp,tyr,phe Solvent accessible area for /A:trp,tyr,phe & aromatic-ring = 7683.3 Solvent accessible area for :trp,tyr,phe (285 atoms) of /A:trp,tyr,phe & aromatic-ring = 7683.3
Which is different from the sum of the values I got before. I think I'm missing something basic on SASA calculations... Also, from your answer to Prathvi, those numbers should be squared Agstrom. Do these number make sense? For a single residue (measure sasa:263, which is a surface-exposed Tyrosine) I got 331.95. Those values are similar to what Prathvi got so am I doing the same mistake? I was expecting, for a single residue something like two order of magnitude less. You said ".. 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. " Does this means that with the commands I typed ChimeraX "Isolates" the residue and calculate the SASA as if it was not included in the protein? Anyway, I think it is clear I'm an unexpert user so If there is any tutorial about SASA on ChimeraX (could not find those, only for Chimera), please, feel free to suggest.
Thank you!! Best, Ale
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#surfac...> 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@cgl.ucsf.edu> wrote:
Hi Elaine, Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues?
Thank you so much Elaine!! On Mon, Nov 14, 2022 at 9:42 PM Elaine Meng <meng@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#surfac...
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@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
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@iitk.ac.in> wrote:
Thank you so much Elaine!!
On Mon, Nov 14, 2022 at 9:42 PM Elaine Meng <meng@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#surfac...
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@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
On Nov 17, 2022, at 8:01 AM, Prathvi Singh via Chimera-users <chimera-users@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@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#surfac...>
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
participants (3)
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alessandro.strofaldi＠gmail.com -
Elaine Meng -
Prathvi Singh