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 > >
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
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
