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
