[Chimera-users] specifying surface atoms

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 24 09:16:31 PDT 2019

Hi Susy,
Besides the video that Omar suggested,

> I recommend you to follow this short tutorial.
> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html
> Best,
> Omar

... see also this previous post “identifying surface residues”:


It describes the same process as shown in the video, as well as possible commands.  First you always have to show the molecular surface.  You can just show it for the whole molecule.

Then, the process is very similar to identify surface atoms instead of whole residues.  In the Select by Attribute dialog, you would just select by attribute of “atoms” instead of “residues”.   You can write a list of selected atoms or residues with menu: Actions… Write List, or you can use the selection in some other command, for example: color red sel

Or if you wanted to use commands to select by area instead of the dialog, that previous post showed an example for residues:

select :/areaSES>30

To use it instead for atoms, could be something like

select @/areaSES>4.0
select @/areaSAS>3.0

… where you would have to decide the minimum value of surface area that you want to use, and whether it should be SAS (solvent-accessible surface) or SES (solvent-excluded surface). 

You can even limit the selection by element or by residue type, for example:

select @/areaSAS>3 & ~C
(select atoms by area and not-carbon)

select @/areaSAS>3 & :asp,glu,his,lys,arg
(select atoms by area and that are also in the named residue types)

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 23, 2019, at 3:35 PM, Susy López <susannalopez18 at gmail.com> wrote:
> Dear all
> This does not answer my question. Maybe, I don't explain it properly.
> I would just like to know if there is any command in Chimera, which allows me to identify the atoms that are part of the total solvent accessible surface area (SAS).
> I will try to explain my question with an example.
> First,
> Commands:
> open 121p
> select :62
> show sel
> Select>residue>all nonstandard
> Actions>Atoms/Bonds>delete
> select :62 at OE1
> surface sel
> <image.png>
> As shown in the image, I have identified an atom that forms the surface accessible to the solvent. However, to identify the total atoms of that protein I have to select atom by atom, which implies a lot of time and more if I have several proteins.
> So, I would like to know, if it´s possible to obtain a command that allows me to select all the atoms at the same time, specifying the atoms that are part of the total solvent accessible surface area(SAS). 
> Thank you (: 
> kind regards,
> Susanna

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