[Chimera-users] Contact area between 2 Proteins

[Fernando Villa]

Thank you very much Dr. Elaine Meng, it has been very helpful.
thank you so much.
Best regards!


ATTE
Fernando Villa Díaz



El vie., 17 de may. de 2019 a la(s) 14:48, Elaine Meng (meng at cgl.ucsf.edu)
escribió:

> Hi Fernando,
> Method 2 in the tutorial already explains this situation.  First it uses
> “measure buriedArea” to get the total buried SAS and also assign values to
> the atoms.  Then it specifies the atoms that have buried SAS > 1.0 square
> angstroms for coloring.  Coloring is just the example, but you could also
> do selection of the atoms with buried SAS greater than some value (doesn’t
> have to be 1.0) and then write out a list of the residues in the selection.
>
> See the coloring commands you already used:
>
> > Command: color yellow #0.1@/buriedSASArea> 1
> > Command: color hot pink #0.2@/buriedSASArea> 1
>
> You could use “select” instead of “color” to select the atoms using their
> buried SAS values, for example:
>
> select @/buriedSASArea> 1
>
> You could use some other value than 1.0.  You will have to decide what you
> want.  The above will select the same atoms that your script colored.
>
> Then you can write a list of the atoms (or the residues containing those
> atoms) with menu: Actions… Write List or command “writesel”, e.g. to a file:
>
> writesel  your-output-file-pathname  itemType residue
>
> …or to the Reply Log:
>
> writesel  -  itemType residue
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html><
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On May 17, 2019, at 12:20 PM, Fernando Villa <fer.vdl1928 at gmail.com>
> wrote:
> >
> > The help that you have given me has generated great advances in my
> project and knowledge about the Chimera 1.13.1 program.
> >
> > I have a question about the functions mentioned above:
> > again if I run the tutorial of measure burried area in this case (SAS):
> >
> > Command: open 1avx
> > Command: ~ longbond
> > Command: split
> > Command: delete solvent
> > Command: surface
> > Command: color sea green # 0.1
> > Command: color medium purple # 0.2
> > command: measure buriedArea # 0.1 # 0.2
> > SAS
> > Command: color yellow #0.1@/buriedSASArea> 1
> > Command: color hot pink #0.2@/buriedSASArea> 1
> > <image.png>
> > Command: alias  ^face-me  set independent;  turn y -90 model  #0.1; turn
> y 90 model  #0.2; ~set independent
> > Command: alias  ^separate  move x $1 model  #0.2; center
> > Command: savepos closed
> > Command: face-me
> > Command: separate 18
> > Command: savepos open
> > surface > hide
> > <image.png>
> >
> >   Could I know which residues participate in the interaction with a
> command line or a script (.py)?
> >
> > for not select manually the residues (to avoid this tedious part)
> >
> > I would greatly appreciate your help!
> >
> > best regards!
> >
> > ATTE
> > Fernando Villa Díaz
>
>
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