I completely agree here, an integrated total platform would be immensely useful. I think that the problem is not necessarily all that far from a solution- currently there is a collaborative computing project for NMR (CCPN)
http://www.bio.cam.ac.uk/nmr/ccp/ The core of this program is the data model in which each atom in a molecule is defined. The next layer are the conversion scripts which take the molecule data from the model and pipe them out to whatever format is needed for the various data manipulation programs (Aqua, XPLOR and the like). Seeing as this model is in existance and will be tightly integrated with the PDB databank for their structural checking procedures prior to accepting a model it would make sense that this be used as an industrial standard. Jules Jules Jacobsen MRC Centre for Protein Engineering Cambridge Laboratory of Molecular Biology On Thu, 12 Dec 2002, Michael Sorich wrote: > Hello all, > > I share in Warren's vision of extending PyMol into a "complete platform > for crystallography, computational chemistry, modeling, and > informatics". However, I believe this can only come about by cooperation > and integration with other python based molecule toolkits. MMTK has code > which may be expanded into a general molecular mechanics engine. Frowns > toolkit allows for detailed chemical analysis based on topology, > including useful tools such as substructure searching (required for > forcefield atom typing). PyQuante allows for Quantum Chemical > calculations. > > It seems to be in everyone's interest to allow easy interoperation > between the toolkits. However, in my experience it is a frustrating and > difficult task, even for relatively simple tasks. > > Does anyone else feel the same frustration? And if so, does anyone have > a solution? > > I believe that a common set of core modules is required. The most > important feature is the molecule. Each toolkit uses a different > molecule, each with a different interface, holding different information > and optimised for specialised work. If a common molecule definition can > be agreed upon by the major authors of the toolkits concerned, > interoperability will be made MUCH easier. Other multipurpose molecular > modelling programs (MOE, Sybyl) seem to get by using a common molecule > definition, so I believe that it is theoretically possible. The aim > would be to define a molecule that contains all the functionality > required for the multiple toolkits and to maintain the interfaces used > by the toolkits as much as possible. > > The question is whether the will exists to do this? Many of the toolkits > are relatively young. I feel that the longer the problem is ignored, the > less likely that it will be possible to combine features from various > toolkits. > > I am interested in other people's thoughts on this matter. > > > Michael Sorich > PhD Student > School of Pharmaceutical, Molecular and Biomedical Sciences > University of South Australia > Email: michael.sor...@postgrads.unisa.edu.au > mike_sor...@hotmail.com > > > > --- > Outgoing mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.408 / Virus Database: 230 - Release Date: 24/10/2002 > > > > ------------------------------------------------------- > This sf.net email is sponsored by: > With Great Power, Comes Great Responsibility > Learn to use your power at OSDN's High Performance Computing Channel > http://hpc.devchannel.org/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
