Re: [Apbs-users] [PyMOL] Strange behaviour with APBS
Biomolecular electrostatics software
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From: Nathan B. <nat...@ma...> - 2008-09-18 01:32:39
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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: pym...@li... > [mailto:pym...@li...] On Behalf Of > Gilles Truan > Sent: Wednesday, September 17, 2008 1:09 AM > To: pym...@li... > 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 > apb...@li... > 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/ |