Obtaining a list of residues that are solvent-accessible
Hello, I am currently employing ChimeraX to study features of a molecule. I am studying ribosomal RNA (rRNA) in the E. coli ribosome using the PDB model 4YBB. We are interested in seeing what residues from the 23S rRNA are solvent-accessible using a probe radius of 3Å. We are wondering if you could give us some advice on how to achieve this. We have tried a few methods we have found online, but they all yield different results. I look forward to hearing from you. Thank you very much in advance. Best, [cid:25bde0d5-3803-4708-9790-94c965927e2c] Luis Antonio Gracia Mazuca Ph.D. Research Associate Department of Chemistry and Biochemistry The University of Texas at El Paso 500 W. University Ave. El Paso, TX 79968 Office: CCSB G.0512A utep.edu<http://utep.edu/>
Hello, Different programs/servers will give different solvent-accessible surface areas (SASA) mostly because of different atomic radii. There is a "measure sasa" command where you can specify probe radius. If you want to change the atomic radii, do it beforehand with "size." The third thing to consider is how you define the problem -- are you considering the protein, waters, etc. as possibly covering the RNA? E.g. if you only wanted to consider the protein as possibly burying parts of the RNA, but not waters, small molecules, etc. a command something like measure sasa (protein | nucleic) probe 3.0 setAttribute true ...would group all the protein and nucleic acids into a single solvent-accessible surface using probe radius 3.0 and set attribute named "area" with the area of each residue. See help for ChimeraX atomic radii defaults, "size" and "measure sasa" <https://rbvi.ucsf.edu/chimerax/docs/user/radii.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> Then you can choose all the residues with "area" greater than some value, depending on what you think is the cutoff for what is exposed or not. e.g. select all the nucleic acid residues with residue attribute "area" greater than 50 (I'm not saying that is the value to use, just an example): select nucleic & ::area>50 See command-line specification by built-in categories and by attribute values <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> ...or select/color the residues interactively on a histogram of the values with "Render/Select by Attribute" (may want to use the "Restrict to selection" after selecting nucleic if you want to omit the protein residues) <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> You can also write a list of the residues and their "area" attribute values with "info residues" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> 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 Jul 16, 2025, at 3:46 PM, Gracia Mazuca, Luis Antonio via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am currently employing ChimeraX to study features of a molecule. I am studying ribosomal RNA (rRNA) in the E. coli ribosome using the PDB model 4YBB. We are interested in seeing what residues from the 23S rRNA are solvent-accessible using a probe radius of 3Å. We are wondering if you could give us some advice on how to achieve this. We have tried a few methods we have found online, but they all yield different results.
I look forward to hearing from you. Thank you very much in advance.
Best,
<Outlook-sznad3mg.png>Luis Antonio Gracia Mazuca Ph.D. Research Associate
Department of Chemistry and Biochemistry The University of Texas at El Paso 500 W. University Ave. El Paso, TX 79968 Office: CCSB G.0512A utep.edu
Hello Dr. Meng, Thank you so much for your prompt response and the help you provided. All of it was invaluably useful. We have used your advice and obtained what we were looking for. We might be contacting you in the near future with follow-up questions. Thank you so much for your time and value. Best, [cid:0f73acd8-ff52-431c-9c3a-338fe0f0b4b8] Luis Antonio Gracia Mazuca Ph.D. Research Associate Department of Chemistry and Biochemistry The University of Texas at El Paso 500 W. University Ave. El Paso, TX 79968 Office: CCSB G.0512A utep.edu<http://utep.edu/> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, July 16, 2025 5:51 PM To: Gracia Mazuca, Luis Antonio <lgraciamaz@miners.utep.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>; Koculi, Eda <ekoculi@utep.edu> Subject: Re: [chimerax-users] Obtaining a list of residues that are solvent-accessible [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] EXTERNAL EMAIL: This e-mail is from a sender outside of the UTEP system. Please forward suspicious emails by using the report button in Outlook or emailing security@utep.edu<mailto:security@utep.edu> Hello, Different programs/servers will give different solvent-accessible surface areas (SASA) mostly because of different atomic radii. There is a "measure sasa" command where you can specify probe radius. If you want to change the atomic radii, do it beforehand with "size." The third thing to consider is how you define the problem -- are you considering the protein, waters, etc. as possibly covering the RNA? E.g. if you only wanted to consider the protein as possibly burying parts of the RNA, but not waters, small molecules, etc. a command something like measure sasa (protein | nucleic) probe 3.0 setAttribute true ...would group all the protein and nucleic acids into a single solvent-accessible surface using probe radius 3.0 and set attribute named "area" with the area of each residue. See help for ChimeraX atomic radii defaults, "size" and "measure sasa" <https://rbvi.ucsf.edu/chimerax/docs/user/radii.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> Then you can choose all the residues with "area" greater than some value, depending on what you think is the cutoff for what is exposed or not. e.g. select all the nucleic acid residues with residue attribute "area" greater than 50 (I'm not saying that is the value to use, just an example): select nucleic & ::area>50 See command-line specification by built-in categories and by attribute values <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> ...or select/color the residues interactively on a histogram of the values with "Render/Select by Attribute" (may want to use the "Restrict to selection" after selecting nucleic if you want to omit the protein residues) <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> You can also write a list of the residues and their "area" attribute values with "info residues" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> 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 Jul 16, 2025, at 3:46 PM, Gracia Mazuca, Luis Antonio via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am currently employing ChimeraX to study features of a molecule. I am studying ribosomal RNA (rRNA) in the E. coli ribosome using the PDB model 4YBB. We are interested in seeing what residues from the 23S rRNA are solvent-accessible using a probe radius of 3Å. We are wondering if you could give us some advice on how to achieve this. We have tried a few methods we have found online, but they all yield different results.
I look forward to hearing from you. Thank you very much in advance.
Best,
<Outlook-sznad3mg.png>Luis Antonio Gracia Mazuca Ph.D. Research Associate
Department of Chemistry and Biochemistry The University of Texas at El Paso 500 W. University Ave. El Paso, TX 79968 Office: CCSB G.0512A utep.edu
participants (2)
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Elaine Meng -
Gracia Mazuca, Luis Antonio