[Chimera-users] surface hydrophobicity display

[Eric Pettersen]

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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