[Chimera-users] Contact area between 2 Proteins

[Elaine Meng]

Dear Fer Villa,
(better to send questions to chimera-users at cgl.ucsf.edu, CC’d here)

It is not really a matter of right and wrong.  Instead it depends on what you want…  

If you want to measure buried solvent-accessible and solvent-excluded surface areas of atomic structures, use “measure buriedArea”.  

The “measure contactArea” command is similar but if the goal is measurement (rather than coloring for a figure), it is generally used for other kinds of surfaces that are not necessarily associated with any atoms, like density map isosurfaces.  In that case, the appropriate cutoff value really depends on the judgment of the user based on what kinds of surfaces these are and what the user is trying to do.

The tutorial you mention is for making a figure where the interaction surfaces of two proteins are colored, which is a different purpose than getting a measurement value.  It explains that different cutoffs could be used with “measure contactArea", but the example has 2.5 because it gave similar appearance to using the other (buriedArea) method.  The tutorial shows both methods because if you are making a figure, you could use either one as you like.  It actually discusses three methods.

For the other people on the list, here is that tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
… 3 methods of coloring the interface:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#interface>

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 10, 2019, at 12:17 AM, Fernando Villa <fer.vdl1928 at gmail.com> wrote:
> 
> Dear Chimera users,
> I would like to know which is the correct method to know what is the surface area of contact between two proteins:
> measure contactArea or measure buriedArea?
> When I apply the command: measure contactArea # 0.1 # 0.2 2.5 color yellow offset 0 that comes in the tutorial, it says that the cutting distance is equal to 2.5 A2
> But, is it correct?
> How can I know that?
> this example states that if this cut-off distance (2.5 A) is applied compared with a cut distance for measure buriedArea:
> Command: measure buriedArea # 0.1 # 0.2
> Command: color yellow #0.1@/buriedSESArea> 1
> Command: color hot pink #0.2@/buriedSESArea> 1
> measure buried Area # 0.1 & protein # 0.2 & protein
> atoms with> 1.0 Å2
> How can I know which is the correct contact area (protein protein interaction) of two models or crystals?
> What is the correct cutting area that I should apply?
> Could it be the default cut area of 1A?
> Which method of calculation is better, measure contactArea or measure buriedArea?
> I would thank you in advance for a possible solution to my problem.
> 
> Best regards.
> 
> Fer Villa.
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> 
> <image.png>
> 
> Command:open 1avx
> Command: ~longbond 
> Command: split
> Command: preset apply int 2 
> Command: repr stick 
> Command: delete solvent 
> Command: color sea green #0.1 
> Command: color medium purple #0.2
> Command: surface    
> Command: measure contactArea  #0.1  #0.2  2.5  color yellow offset 0 
> Command: measure contactArea  #0.2  #0.1  2.5  color hotpink offset 0
> 
> 
> or 
> 
> Command: measure buriedArea  #0.1  #0.2 
> Command: color yellow  #0.1@/buriedSESArea>1 
> Command: color hot pink  #0.2@/buriedSESArea>1  
> 
> Command: measure buriedArea  #0.1&protein  #0.2&protein  
> 
> ATTE
> Fernando Villa Díaz
>