[Jmol-developers] [ jmol-Feature Requests-1710595 ] support for PQR

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Feature Requests item #1710595, was opened at 2007-05-01 14:32
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Category: New IO Format
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Angel Herraez (aherraez)
Assigned to: Nobody/Anonymous (nobody)
Summary: support for PQR

Initial Comment:
It would be interesting to add support for opening files in the PQR format. This is a derivative of PDB that adds charge and radius. PDB is converted to PQR by PDB2PQR and derivatives, programs that estimate charge distribution (and also add hydrogens). PQR is then used as input by APBS, a program that calculates molecular electrostatic map and exports it in DX format, which can be used by Jmol to color a molecular surface.
PQR keeps most of the PDB format except that it puts charge more or less in the occupancy location, and radius shifted but close to the B factor location.

The addition of hydrogens and the calculation of charges make this format interesting to be read by Jmol.

Description of the PQR format is at http://apbs.sourceforge.net/doc/user-guide/index.html#pqr-format
There are plain text and XML variants.

(Note> I have detected some problems with added hydrogen atoms labelled e.g. HG22, which are interpreted as mercury by Jmol due to column shift, but for the rest the files are read OK, except that color temperature is incorrectly interpreted, due to wrong columns.)

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You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1710595&group_id=23629