[chimerax-users] render buriedArea surface?

[Elaine Meng]

Sorry about that, I didn’t read my own description of ChimeraX “measure buriedarea” carefully enough!
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea>

However, with the ChimeraX “contacts” command “select” option you can select down to the specific contacting atoms, rather than only whole residues.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html#options>

Elaine

> On Sep 9, 2019, at 4:20 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> The select option of the ChimeraX measure buriedarea selects whole residues, not single atoms.  So your method of coloring will color the entire surface patch for a residue.  There is no option to select individual atoms by buried area which would give finer granularity.
> 
> 	Tom
> 
> 
>> On Sep 9, 2019, at 4:14 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Alexis,
>> That is true.  There’s no way in ChimeraX commands to specify only a subset of an atomic patch of the surface. The whole patch for the atom is affected at once.  
>> 
>> You could try doing it in Chimera using tutorial method 3 of coloring the interface, which uses surface proximity rather than atomic divisions.  I don’t know of any equivalent in ChimeraX to the Chimera “measure contactArea” command used in this method.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#interface>
>> 
>> It is unclear, however, if these relatively small distinctions really have a biological meaning, or what the most meaningful cutoff value for “measure contactArea” would be.  You can get a large difference in ChimeraX by just varying the “measure buriedarea” cutoff, as well.
>> 
>> I don’t think you can clearly see very much from the displayed surface because the SES is quite different from SAS, especially in the crevices that may occur around interfaces.
>> Best,
>> Elaine
>> 
>>> On Sep 9, 2019, at 3:58 PM, Alexis Rohou <a.rohou at gmail.com> wrote:
>>> 
>>> Thanks Elaine,
>>> 
>>> I wonder if I am missing something, but I'm not sure how the atom-selection-based methods can be used to accurately depict the buried surface area. The problem is that an atom is either in the selection or out of it, and then all of that atom's surface gets colored, not the just the regions of the surface that were buried.
>>> 
>>> See for example this screenshot:
>>> <image.png>
>>> 
>>> Here, I wanted to color the buried surface between the yellow chain and the purple one. I followed the method you outlined , which correctly identified that most of the atoms for the Tyr side chain I am showing are involved in a contact with the purple chain. But clearly, not all the blue surface is buried by the purple chain - only the "top" and "left parts of it, in this view.
>>> 
>>> For the record, here's what I did:
>>> color #1 fromatoms target s transparency 50
>>> measure buriedarea name_yellow with name_purple sel true cutoff 60
>>> color sel & name_yellow  blue target s transparency 50
>>> 
>>> Am I misunderstanding something? Or in fact, should I just use method #3 from the Chimera tutorial instead?
>>> 
>>> Thanks for your guidance!
>>> 
>>> Cheers,
>>> Alexis
>>> 
>>> 
>>> 
>>> On Mon, Sep 9, 2019 at 10:27 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> There’s a nice diagram explaining SAS vs. SES in the “surface” manpage:
>>> 
>>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#top>
>>> 
>>>> On Sep 9, 2019, at 10:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>> 
>>>> 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
>>>> 
>>>> 
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