[Chimera-users] surface hydrophobicity display
meng at cgl.ucsf.edu
Thu Feb 3 11:02:55 PST 2011
Hello Sumitro et al.,
Dr. Efremov, whose group produces the PLATINUM server, pointed out that you can get a dot surface of the protein by uploading it as the "ligand" and not uploading any "receptor."
PLATINUM server: <http://model.nmr.ru/platinum/>
When I tried this with my example protein, it worked fine if I set the surface dot density to "low" or "very low" *before* launching the calculation. Using the default "medium" gave an incomplete surface even though the file was extremely large -- probably some memory limit was reached. (To prepare the example input with Chimera, I opened 2gbp, deleted ligand and waters, added hydrogens, saved PDB file). The server said 2 ligand files were uploaded, but I just ignored that.
After the PLATINUM calculation is done, click the floppy disk icon for the "ligand" that is really your protein, save as "molecular surface" of type "PDB surface." It may several seconds to respond or write the file because even at low density, there are lots of dots.
That gives a file in PDB format of dots as "atoms" with hydrophobicity potential in the bfactor column, for coloring with Render by Attribute in Chimera, or with the command "rangecolor".
For display in Chimera it would still be better to get the whole 3D grid of potential values -- grid data could be used to color a solid surface instead of just dots, or to show isopotential contours. Dr. Efremov kindly said that they will take a look at maybe adding another grid format. For now, it is possible to show the protein hydrophobicity potential by coloring its own dot surface as described above.
On Feb 1, 2011, at 11:06 AM, Elaine Meng wrote:
> I already did that. It is a dot surface of the ligand only where each dot is a PDB "atom". So you can see dots of the ligand surface colored by the potential from the receptor, but not the surface of the receptor which is what we were more interested in (at least, that's what I was interested in).
> On Feb 1, 2011, at 10:59 AM, Eric Pettersen wrote:
>> According to the PLATINUM paper:
>> Also, additional output is provided for more detailed analysis of selected ligands/ligand poses which will be discussed below. To perform subsequent analysis, the MHP data for each ligand can be downloaded in one of the following formats.
>> • Simple text file where atoms are annotated according to the MHP atom type parameterization.
>> • The pdb file where either atomic hydrophobicity constants or surface MHP values are written to the B-factor column.
>> • Ligand molecular surface represented as a set of dots in pdb or InsightII (Molecular Simulations Inc., 2000) formats.
>> • Grid hydrophobic/hydrophilic potential in InsightII or MolMol (Koradi et al., 1996) formats.
>> It would seem that from the second part of #2 that you could get the surface MHP values into the B-factor column (and then use Render By Attribute...)
>>> PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes.
>>> Pyrkov TV, Chugunov AO, Krylov NA, Nolde DE, Efremov RG.
>>> Bioinformatics. 2009 May 1;25(9):1201-2.
>>> Today the PLATINUM web server exists! I can't quite get what I want for viewing in Chimera, however:
>>> Their user manual explains how to download data for display in other programs, including PDBs with the atomic hydrophobicity constants in the B-factor column. I can open those in Chimera and use Render by Attribute to show the values. The constants are only the starting data, however, not the potential...
>>> Unfortunately I can't get a potential map of the receptor that can be used in Chimera. Platinum is quite ligand- or docked-molecule-centric. You can get molecular surface dots in PDB format with the potential as the "bfactor" but it is only for the surface of the ligand, not the receptor. The potential can also be output as a 3D grid, but in some formats Chimera does not read (InsightII or MolMol), and I suspect the grid might be only in the location of the ligand, not enclosing the whole protein receptor.
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