[Chimera-users] Contact area between 2 Proteins

[Elaine Meng]

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