Nathan, Strictly speaking, the issue may be with PDB2PQR itself, not APBS. Furthermore, we don't yet know whether a combined development version of all three packages would still reproduce the problem.
As an aside, a good reason for PyMOL to see PQR files is for diagnostic visualization: to enable the user to inspect and modify or manipulate what is being fed directly into APBS. PyMOL can read & write PQR directly, though we may have issues reading non-PDB-like PQR files. I would generally agree that use of PDB2PQR to convert PDBs to PQRs is the preferred route, since PyMOL doesn't do any checking or optimization. Anyway, based on reported symptoms alone, the problem appears to be that some component in the PyMOL->APBS pipeline assumes that the input PDBs are space-delimited rather than column-delimited. This guess is based on the observation that a B-factor of 100 or greater eliminates the space between the occupany and the B factor in spec-compliant PDB files, and the calculation fails. As a starting point for troubleshooting, I just pulled current pdb2pqr source from trunk and CANNOT reproduce the problem, so either this is already a solved problem with current code, or something else is going on. Gilles, what versions of PyMOL and APBS are you using? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -----Original Message----- From: Nathan Baker [mailto:nathanaba...@mac.com] Sent: Wednesday, September 17, 2008 6:28 PM To: DeLano Scientific Cc: gilles.tr...@cgm.cnrs-gif.fr; pymol-users@lists.sourceforge.net; apbs-us...@lists.sourceforge.net Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS Hi Warren -- The PQR format (which doesn't really have a standard) is basically just whitespace delimited. I'm curious, though -- why would a PyMOL APBS invocation ever see the PDB file? Wouldn't a user first convert it to PQR with PDB2PQR (ideally) or with PyMOL's built-in functionality? Thanks, Nathan On Sep 17, 2008, at 2:21 PM, DeLano Scientific wrote: > Gilles, > > The PyMOL and APBS programs have differing views as to whether PDB & > PQR files are column-based or space-delimited, respectively. We must > eventually sort this out, because it causes continued grief for our > users in common. > > For now, however, the workaround is to make sure no B-factors exceed > 100. > > alter all, b=min(b,99.9) > > should about do it. > > Cheers, > Warren > > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Gilles > Truan > Sent: Wednesday, September 17, 2008 1:09 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Strange behaviour with APBS > > I have noticed a strange behaviour of the APBS module. I used it a lot > recently and it works perfectly for 95% of the structures I analyzed. > I usually fetch the pdb code, then remove waters, heteroatoms and so > on. I also noticed that in some cases, when the b factor is quite big > (over > 100) APBS cannot work the pdb file because it mixes up the b factor > and the number which is just before (occupancy). But I managed with > that, I usually erase the b factor to 0 before doing the APBS > calculation and everything works fine then. > The other strange behavious is related to nothing I can pinpoint > unfortunately. For some files (I always fetch them with the fetch > command from Pymol), I can set the grid OK and when I launch APBS, I > can see the file being processed (I see the select and hydrogens go > on!) and then it stops with the following error message: > > ObjectMapLoadDXFile-Error: Unable to open file! > ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? > > All the paths for APBS are correctly setup, the temp files are setup > as well. > If I then fetch a new file, APBS works, even for several files (one > after > another) and if I come back to the file I wanted to do first, it gives > me the same error message (BTW, the pdb file is 1CJC). > > Any help would be greatly appreciated!!! > > > ---------------------------------------------------------------------- > --- This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge Build the coolest Linux based applications with Moblin SDK & > win great prizes Grand prize is a trip for two to an Open Source event > anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apbs-us...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/
