[Chimera-users] surface hydrophobicity display

[Elaine Meng]

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).
Elaine

On Feb 1, 2011, at 10:59 AM, Eric Pettersen wrote:

> On Feb 1, 2011, at 10:20 AM, Elaine Meng wrote:
> 
>> 
>>> On Jan 31, 2011, at 9:55 AM, Elaine Meng wrote:
>>>> 
>>>> -- the following web server sounded promising, but apparently no longer exists:
>>>> 
>>>> 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.
>>>> <http://www.ncbi.nlm.nih.gov/pubmed/19244385>
>>>> 
>> 
>> 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...
> 
> 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...) though some perfunctory poking around the PLATINUM manual didn't reveal to me how to do that...
> 
> --Eric
> 
>> 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. 
>> Elaine
>> 
>> 
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