Charles, ".dat" is a hopefully oversubscribed file extension, and the .dat which PyMOL currently recognizes is for Macromodel. If you are have some development skills, consider writing a Python-based CSD file parser for the Chemical Python portion of PyMOL. Any ChemPy model can be loaded straight into PyMOL. This approach doesn't have quite the performance as native C reads but, it will suffice for moderate-throughput applications.
Example Python code for reading MOL files can be found in modules/chempy/mol.py. The code is just over 105 lines and supports both reads and writes. One should be able to add a CSD reader with just an hour or two starting with a description of the CSD file format. Just focus on the atom symbols, coordinates, bonds, and bond orders...the rest can be dealt with later on. I propose using the extension ".csd" for csd structure files. Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. > From: Ross, Charles [mailto:charles.r...@stjude.org] > > I am running latest version (0.73) on an SGI Octane running > IRIX 6.5.14m. > Structures extracted from the Cambridge Structural Database have the > extension .dat. This extension is recognized by PyMol, > although perhaps not > as a structure file - when I read it, I get no errors, but I get no > structure either. Does PyMol recognize CSD structure files, > and if so, what > is the proper extension? > > thanks > Charles Ross > > Department of Structural Biology > St. Jude Children's Research Hospital > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
