> 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 >
