Feature Requests item #1710595, was opened at 2007-05-01 07:32 Message generated for change (Comment added) made by hansonr 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: Bob Hanson (hansonr) Date: 2007-05-01 08:49 Message: Logged In: YES user_id=1082841 Originator: NO What you mean, I think, is that Jmol is almost reading the PQR format, but not quite. From that reference site I see: A.1.1. PQR flat-file format This format is a modification of the PDB format which allows users to add charge and radius parameters to existing PDB data while keeping it in a format amenable to visualization with standard molecular graphics programs. The origins of the PQR format are somewhat uncretain, but has been used by several computational biology software programs, including MEAD and AutoDock. UHBD uses a very similar format called QCD. But no actual specification of the format. I'm quite concerned about this comment: APBS reads very loosely-formatted PQR files: all fields are whitespace-delimited, thereby allowing coordinates which are larger/smaller than ± 999 Å. APBS reads data on a per-line basis from PQR files using the following format: But if that is the case, then it's hard to see how this is compatible with PDB format, where fields are column-designated for a good reason - they often have no intervening space. For example, the files are limited to fewer than 10000 atoms. Ah, but at least in relation to APBS I read at http://cholla.wustl.edu/baker/classes/nbcr/user-guide/a2578.html : The "cost" of this looser formatting is the inability of APBS to parse PQR files with chain IDs. These fields need to be removed from PQR files before they are used with APBS. From I read: What is a PQR file? 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). But we have from Angel's example: ATOM 1 N THR 1 46.148 16.581 2.104 0.1812 1.8240 and from PDB: ATOM 2707 CG2 ILE A 339 13.681 44.682 -10.781 1.00 48.45 C 0 1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890123456789 Not obvious because SourceForge puts this in Helvetica, but I think they don't do as advertised. They have not just "used the temperature and occupancy columns" They have moved the columns and deleted the (crutial) element symbol column. If Jmol is to read this we need: 1) The actual file specification. Where is that specified? 2) Whether or not the XML version is specified. All I see at APBS is a vague reference to the data they need. 3) Some way to distinguish these from PDB files. This would either require a new "format" keyword for the load command, which I've thought we should have anyway, or some parameter such as "loadFormat" that would bypass the current method Jmol uses to discover a file format. Not saying it isn't possible. Just not trivial. Bob ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2007-05-01 08:04 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 07:36 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
