[chimerax-users] render buriedArea surface?

[Elaine Meng]

Hi Alexis,
The “measure buriedarea” command has a “cutoff” option that can be used with its “select” and/or “color” options to select and/or color atoms with more than the specified cutoff area buried.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea>

If you use the selection approach, you can then color the corresponding patches within the molecular surface, or hide the rest of the surface, etc.  For example, 1avx trypsin complexed with trypsin inhibitor:

open 1avx
split
measure buriedarea /a&protein with /b&protein sel true cutoff 5
surf
color sel & /a red target s
color sel & /b yellow target s

Note that “measure buriedarea” values are SASA (solvent-accessible surface area) whereas the displayed surface is instead the SES (solvent-excluded surface).  Larger cutoff values will select smaller patches that look more like the touching parts of the SES.  The “&protein” stuff is needed so that waters are not included in the calculation.  Alternatively, you could “delete solvent” first.

There are other ways to select the contacting atoms, e.g. with the “contacts” command, but this is the way based on surface area.

There is a Chimera (not ChimeraX) tutorial that does exactly this same thing, with three different ways of identifying the interface atoms, and several other steps for making a figure to show the interface-surface coloring, like opening the interface like a book:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>

The ChimeraX approach I outlined above is slightly different than method 2 in that tutorial, but also based on surface area.  Method 1 in that tutorial is analogous to using ChimeraX “contacts” command, but there is no ChimeraX equivalent for method 3.  

The other steps like opening the interface like a book can also be done in ChimeraX but the commands and/or their syntax would be different:  ChimeraX does not have “set independent” for independent rotation, but relevant commands would be: move, turn, view name, view.  In the example above, I used “split”  so that the two chains are two models that can be moved separately with the move and turn commands.  You don’t need split to do the coloring above, but I saw that doing split afterward nuked the existing surfaces, which would defeat the purpose.

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 9, 2019, at 9:27 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
> 
> Hi all,
> I would like to depict the buried surface area between two chains. I have used "measure buriedarea" to measure it, and I can use "surface" to display the surfaces of either set of atoms, but I'd like to depict the surface of one of the chains, highlighting the region buried by the other chain. 
> 
> Is there a way to do this in ChimeraX? 
> 
> If not, does anyone have a recommendation as to how to achieve this? Perhaps by pre-computing the surfaces in another program?
> Thanks in advance!
> Cheers,
> Alexis