Gaussian surface visualization of a subset of residues
To whom it may concern, I am a PhD student at the Biomedical Genomics Lab at the Institute of Biomedicine of Barcelona. I am using ChimeraX to produce figures for the publication of an in-house recently developed tool for cancer driver gene discovery. I am new to using ChimeraX, so I am sorry if my question might seem very naive to you. Anyway, I can't find this information anywhere else. My problem is simple: I want to show the surface (or volume) occupied by the atoms of a selected number of residues within a chain. I can easily achieve this by using the Gaussian surface (GS) by adding the parameter "resolution" to the "surface" command as "surface :10-20 resolution 6" The problem is that the surface visualized in this way has "gaps" where it overlaps with other atoms that are not from the selected residues. As expected, these gaps get larger when using a greater resolution. Now, I would like to show the complete surface around these residues, without gaps. Could you please provide any suggestions? Thank you in advance, and best regards, Stefano Pellegrini -- *Stefano Pellegrini, **PhD student* Barcelona Biomedical Genomics Lab Institute for Research in Biomedicine (IRB) Carrer de Baldiri Reixac 10, 08028, Barcelona, Spain http://bbglab.irbbarcelona.org
Hi Stefano, You do not need to use a Gaussian surface (although you can if you want) -- that is a completely separate issue. Regardless of which type of surface you show, the "enclose" option is what you want. Normally people do not not want to the surface to completely enclose the atoms, they just want to see the surface contributed by those atoms in the context of the whole molecule. However, to enclose them, you could use like this: surface :10-20 enclose :10-20 -- OR, if you wanted Gaussian, something like -- surface :10-20 enclose :10-20 resolution 6 See the surface help for descriptions of all the options. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 13, 2023, at 6:23 AM, Stefano Pellegrini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
To whom it may concern,
I am a PhD student at the Biomedical Genomics Lab at the Institute of Biomedicine of Barcelona. I am using ChimeraX to produce figures for the publication of an in-house recently developed tool for cancer driver gene discovery. I am new to using ChimeraX, so I am sorry if my question might seem very naive to you. Anyway, I can't find this information anywhere else.
My problem is simple: I want to show the surface (or volume) occupied by the atoms of a selected number of residues within a chain. I can easily achieve this by using the Gaussian surface (GS) by adding the parameter "resolution" to the "surface" command as "surface :10-20 resolution 6" The problem is that the surface visualized in this way has "gaps" where it overlaps with other atoms that are not from the selected residues. As expected, these gaps get larger when using a greater resolution. Now, I would like to show the complete surface around these residues, without gaps. Could you please provide any suggestions?
Thank you in advance, and best regards, Stefano Pellegrini
participants (2)
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Elaine Meng -
Stefano Pellegrini