[Chimera-users] colouring according to hydrophobicity

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 28 08:26:17 PST 2013


Hi Dieter,
Yes, both can be done!

(1) In the case of hydrophobicity, in Chimera this is not treated as a "potential" that varies in space, but a simple lookup where the Kyte-Doolittle hydrophobicity value for each amino acid type is mapped to coloring of the atoms (and/or ribbons and/or molecular surface) of that amino acid. You can also use other scales besides Kyte-Doolittle hydrophobicity with a little more effort, but the Kyte-Doolittle one is built in as the Chimera residue attribute "kdHydrophobicity".  With coloring by atom or residue attribute, you can first color the atoms (Tools... Structure Analysis... Render by Attribute or command "rangecolor"), then color the volume isosurface to match the closest atoms with Color Zone (Tools... Volume Data... Color Zone).

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> 

(2) In the case of charge distribution, you could literally color the atoms by their partial charge values (atom attribute "charge") after using Add Charge in Chimera and then proceed as outlined above, but probably instead you mean to color by the electrostatic potential (ESP).  If so, you would first calculate an ESP map from the atomic structure and then directly color the volume isosurface by the map with Electrostatic Surface Coloring (Tools... Surface/Binding Analysis... Electrostatic Surface Coloring).

There are multiple possibilities for how to generate the ESP map: 
(2a) outside of Chimera with Poisson-Boltzmann solver: DelPhi, APBS, or UHBD
(2b) in Chimera using Coulombic Surface Coloring or command "coulombic" with option to calculate grid turned on; the grid is the ESP map. The GUI but not the command requires you to first display the molecular surface (which of course could be hidden later).
(2c) in Chimera using interface to APBS (you would probably first use the Chimera interface to PDB2PQR, and then use the result from that as the input to APBS)

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

Also see this image tutorial. Although it's about coloring the molecular surface rather than a volume isosurface, there are examples of hydrophobicity, Coulombic ESP, and Poisson-Boltzmann ESP coloring:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 28, 2013, at 6:37 AM, Dieter Blaas wrote:

> Hi,
>    I am wondering whether there is any (easy) way of colouring a volume (e.g. an MRC file made from a pdb file and filtered to say, 10 A with e.g. xmipp)  according to hydrophobicity (using the values derived from the amino acid residues in the pdb file)? I am aware of the way to colour the van der Waals surface but the resolution is somewhat too high not allowing to get a more general view, for example whether the molecule is more hydrophobic on one side than on another side. The same question applies to the charge distribution....
> 
> Thanks, Dieter




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