Calculating solvent accessible surface area for all residues in a protein?
Hi!
Is there a way to calculate the solvent accessible surface area (SASA) for every residue in a protein (5FTL) and output the result to a text file? I am trying to rank order residues by their accessibility.
I know I can use the command line to calculate one residue at a time but it's laborious. Is there a way to automate the process or a GUI shortcut?
Thanks! Chad
Hi Chad, If you use "measure sasa" with the "setAttribute true" (which is actually the default) it will create per-atom and per-residue attributes named "area", see:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa
... and then you can write the values out by saving an attribute file:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes
Example:
open 5ftl measure sasa protein save ~/Desktop/5ftl-residue-areas.defattr attrName r:area
Note that the solvent-accessible area is based on lumping all specified atoms together. So even if there are multiple protein chains, the above would just treat the protein as one lump. If you want areas in the context of each chain (a residue might be on the surface of one chain but buried in the interface between it and another chain) you would need to specify a single chain instead of "protein" in a series of measure commands.
Also note that this procedure does not normalize the values by fully exposed area. You just get square angstroms, not % accessibility.
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, 2023, at 6:46 PM, Altobelli, Chad via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi! Is there a way to calculate the solvent accessible surface area (SASA) for every residue in a protein (5FTL) and output the result to a text file? I am trying to rank order residues by their accessibility.
I know I can use the command line to calculate one residue at a time but it's laborious. Is there a way to automate the process or a GUI shortcut? Thanks! Chad
Thank you so much! It worked great. I especially appreciate that you spelled out the commands and limitations.
Cheers, Chad ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, November 15, 2023 8:28 AM To: Altobelli, Chad Chad.Altobelli@ucsf.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Calculating solvent accessible surface area for all residues in a protein?
Hi Chad, If you use "measure sasa" with the "setAttribute true" (which is actually the default) it will create per-atom and per-residue attributes named "area", see:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa
... and then you can write the values out by saving an attribute file:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes
Example:
open 5ftl measure sasa protein save ~/Desktop/5ftl-residue-areas.defattr attrName r:area
Note that the solvent-accessible area is based on lumping all specified atoms together. So even if there are multiple protein chains, the above would just treat the protein as one lump. If you want areas in the context of each chain (a residue might be on the surface of one chain but buried in the interface between it and another chain) you would need to specify a single chain instead of "protein" in a series of measure commands.
Also note that this procedure does not normalize the values by fully exposed area. You just get square angstroms, not % accessibility.
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, 2023, at 6:46 PM, Altobelli, Chad via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi! Is there a way to calculate the solvent accessible surface area (SASA) for every residue in a protein (5FTL) and output the result to a text file? I am trying to rank order residues by their accessibility.
I know I can use the command line to calculate one residue at a time but it's laborious. Is there a way to automate the process or a GUI shortcut? Thanks! Chad
participants (2)
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Altobelli, Chad -
Elaine Meng