Hi Warren --
That's fantastic news! It sounds like a great plan; please let me
know if we can do anything to help out, particularly with the
interface, annoying "ObjectMapLoadDXFile-Error" messages and related
verbosity, etc.
Thanks!
-- Nathan
On Sep 18, 2008, at 2:32 PM, DeLano Scientific wrote:
This might be a good reason to start moving towards distribution of
APBS and PDB2PQR with PyMOL! :)
Indeed, along those lines, here is the plan:
Starting with PyMOL 1.2, we will start distributing an accompanying
open-source compilation named FreeMOL, which includes several
packages many
users would like to be able to call upon when using PyMOL. They are:
(a) an electrostatics package (APBS / PDB2PQR of course).
(b) an MMFF forcefield & minimizer (mengine) for small molecule
building and
peptide modeling.
(C) an MPEG movie generator (mpeg_encode, most likely).
In each case, we are doing the upfront compilation, integration, and
testing
to ensure that what ships actually interoperates reliably, on Mac, on
Windows, and on Linux. With this effort, I am determined that we
will get
to a point where all this stuff "just works" together without major
issues.
Well. That is the plan at least. Nothing in software can ever be
taken for
granted until it has shipped. At present, we about two thirds of
the way
there, so hopefully the rest will have come together before the end
of the
year. Betas will be out much sooner of course...
By the way, just to be absolutely crystal clear: FreeMOL is and
will remain
a 100% free-software open-source project, distributed under full
compliance
with each component's own open-source licensing terms. As such,
FreeMOL is
and must be kept well-separated from our closed-source PyMOL
derivatives.
Cheers,
Warren
PS. I suspect I am not the only one looking forward to the day when
we stop
seeing all those repeated "ObjectMapLoadDXFile-Error"s clogging up
the APBS
& PyMOL mailing lists...
-----Original Message-----
From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-
boun...@lists.sourceforge.net] On Behalf Of Nathan Baker
Sent: Thursday, September 18, 2008 11:54 AM
To: DeLano Scientific
Cc: apbs-us...@lists.sourceforge.net; gilles.tr...@cgm.cnrs-gif.fr;
pymol-
us...@lists.sourceforge.net
Subject: Re: [PyMOL] [Apbs-users] Strange behaviour with APBS
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
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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/
