Feature Requests item #1710595, was opened at 2007-05-01 14:32 Message generated for change (Comment added) made by aherraez You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1710595&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. 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.) ---------------------------------------------------------------------- >Comment By: Angel Herraez (aherraez) Date: 2007-05-01 15:04 Message: Logged In: YES user_id=1065324 Originator: YES I am puzzled: the official PDB2PQR page http://pdb2pqr.sourceforge.net/userguide.html says "A PQR file is a PDB file with the temperature and occupancy columns replaced by columns containing the per-atom charge (Q) and radius (R)." However, when I run a PDB file (1fas) through the PDB2PQR server, I get a file that in the occupancy columns has positive and negative values, -1.0 to +1.0, which must be charges, and the temperature (B factor) columns are partially covered by thos and partially (one position to the right of decimal point) filled with values that look like the radii. I will try to find out more with the PDB2PQR people. ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2007-05-01 14:36 Message: Logged In: YES user_id=1065324 Originator: YES Example PQR file File Added: 1FAS.pqr ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1710595&group_id=23629 ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
