Hi Warren --
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.
This might be a good reason to start moving towards distribution of
APBS and PDB2PQR with PyMOL! :)
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.
I agree completely. However, I think we can remain flexible with the
PQR format while still allowing this.
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.
OK.
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.
This seems like a reasonable guess but I can't think of a component of
PDB2PQR that is sensitive to this. Gilles, can you confirm that you
used PDB2PQR to generate the PQR file for your calculation?
Thanks,
Nathan
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/
--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/
