Choosing solvent exposed residues automatically
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
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 ... ... in pretty good agreement with MLP coloring, e.g. mlp surfaces #1.3 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: 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@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
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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Sincerely yours Yaikhomba
participants (2)
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Elaine Meng -
Mutum Yaikhomba