[Chimera-users] surface hydrophobicity display

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 1 10:20:48 PST 2011

> 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...

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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