[chimerax-users] Choosing solvent exposed residues automatically

[Mutum Yaikhomba]

Hi Elaine

Thanks for this simpler method - I will try this and get back.

Thanks
Yaikhomba


On 07.09.2020 22:51, Elaine Meng wrote:
> I should mention that the "defattr" command that reads attributes from
> file is not in ChimeraX version 1.0.  This feature was added around
> August 18, so you would need to use a daily build from later than
> that, or the 1.1 release candidate.
> Best,
> Elaine
> 
> Change log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>
> 
> 
>> On Sep 7, 2020, at 8:50 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Yaikhomba,
>> Depends what you mean by quick, but there are certainly better ways 
>> than choosing them one by one!
>> 
>> I would use "measure sasa" to define an "area" attribute of residues, 
>> then assign residue hydrophobicities from a file with the "defattr" 
>> command, and then use a single "select" command to intersect these two 
>> attributes.
>> 
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html>
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes>
>> 
>> In the "defattr" example files I already happened to include a file 
>> kdHydrophobicity.txt to assign Kyte-Doolittle hydrophobity, as well as 
>> for several other hydrophobicity scales.  Just download whichever 
>> one(s) you want to try from the links here:
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html#examples>
>> 
>> The commands could be something like:
>> 
>> open 6g2j
>> measure sasa protein
>> defattr ~/Desktop/kdHydrophobicity.txt
>> select ::area>25 & ::kdHydrophobicity>0.0
>> surface protein enclose protein
>> color sel magenta
>> 
>> ... which looks like this ...
>> <two.png>
>> 
>> ... in pretty good agreement with MLP coloring, e.g.
>> 
>> mlp surfaces #1.3
>> <three.png>
>> 
>> In the select command you may want to experiment with the surface-area 
>> and hydrophobicity cutoffs, as well as which hydrophobicity scale you 
>> use.  I didn't try a lot of values for surface-area cutoff, but here 
>> is with all residues with values >25 colored red, reasonable at least 
>> as a first approximation:
>> 
>> <one.png>
>> 
>> 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 6, 2020, at 3:26 PM, Mutum Yaikhomba 
>>> <mutum.yaikhomba at mrc-mbu.cam.ac.uk> wrote:
>>> 
>>> Hi
>>> I am working with a very big pdb model: pdb - 6g2j. I was wondering 
>>> if there is a quick way to select all residues (surface residues) 
>>> that are exposed to the solvent (including those facing the 
>>> membrane)? This is instead of going over each residue one by one and 
>>> selecting them.
>>> 
>>> Additionally, say you have selected these solvent-exposed residues 
>>> and now you want to filter them based on Hydrophobicity - is there a 
>>> way to filter based on the standard Kyte-Doolittle Hydrophobicity 
>>> index for these residues?
>>> 
>>> If there is, it would be of great help and very much appreciated.
>>> Thanks
>>> Yaikhomba
>> 
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-- 
Sincerely yours
Yaikhomba