Re: [PyMOL] Pymol and Autodock
On Thu, 6 Feb 2003, Chris wrote: A couple of quick questions for anyone running Pymol and Autodock. 1. Doing Get dockings in autodock writes out a PDB formatted file, and uses the ` MODEL ' and ` ENDMDL ' records to denote the different dockings is there anyway to get pymol to read these as individual states ? - If not PyMOL does support the MODEL and ENDMDL tags, but so far they've only been tested with NMR structures (as far as I know). With different ligands in one PDB file, it may be necessary to force PyMOL treat each state as a separate entity using the discrete=1 flag. load ligands.pdb,discrete=1 Unfortunately, reading of MODEL and ENDMDL records is not (yet) optimized, so this might bog down. Read-in performace would be better if you could convert your multiligand PDB file to an SD file. does anyone know of a program that will read these files (other than autodock tools (For some reason Autodocktools comes back with strange OpenGl errors (very odd seen as Pymol works great on my wee linux box)) . 2. Is there anyway to directly import Trajectory files (.trj) from simulated annealing dockings into Pymol ? for doing animations in Pymol No, but you might be able to use PyMOL's chempy models to create your own (depending on how easy/hard it would be to read .trj files in Python. Warren
RE: [PyMOL] Pymol and Autodock
SD is a file format for small molecule ligands based around the MDL MOL file (CTAB core). http://www.mdli.com/downloads/literature/ctfile.pdf Advantages: simplicity easy to parse supported by most cheminformatics packages captures valence, stereochem, charge 2D or 3D more extensible than PDB (arbitrary tags) Disadvantages: 999 atom limit (only useful for small molecules!) no standard conventions for storing of atom names or types. fixed field lengths Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: Alan Wilter Sousa da Silva [mailto:a...@biof.ufrj.br] Sent: Thursday, February 06, 2003 7:41 AM To: DeLano, Warren Cc: Chris; PyMOL-users Subject: Re: [PyMOL] Pymol and Autodock On Thu, 6 Feb 2003, Warren L. DeLano wrote: Read-in performace would be better if you could convert your multiligand PDB file to an SD file. Sorry, what's SD? TIA, Cheers, --- Alan Wilter S. da Silva --- Laboratório de Física Biológica Instituto de Biofísica Carlos Chagas Filho Universidade do Brasil/UFRJ Rio de Janeiro, Brasil
