[Chimera-users] specifying surface atoms

[Susy López]

Dear Dr. Elaine Meng

Thank you, thank you very much!!!. I'm very grateful. Finally I could, it
helped me a lot.

Dear Omar

Really, thank you (:

King regards,
Susy

El mar., 24 sept. 2019 a las 11:16, Elaine Meng (<meng at cgl.ucsf.edu>)
escribió:

> 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”:
>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html>
>
> 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
> or
> 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
> -----
> 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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