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!!!
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Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/
