Hi Pawel, 1. PyMOL might have a bug here, or at least the amber file support is rather limited at the momemt. Also note that the amber restart file is not a trajectory but contains only one frame. PyMOL internally treats rst and crd the same (which we should change, actually). So this will work for a proper formatted restart file:
PyMOL> load ../Cdp_UCM.rst7, CDP, 1, crd 2. the load_traj command has an "interval" argument: PyMOL> load_traj ../Cdp_UCM.dcd, CDP, 1, interval=10 You'll always get a quick hint about the command arguments like this: PyMOL>load_traj ? Cheers, Thomas Pawel wrote, On 07/30/13 22:42: > Hello Pymol Users. I just started getting into Pymol and encountered two > issues I'd like to ask about. > > 1. When trying to load amber topology and coordinate files that do not > have the default extension, I get this error: > > PyMOL>load ../Cdp_UCM.prmtop, CDP, 1, top > ObjectMolecule: Attempting to read Amber7 topology file. > CmdLoad: "../Cdp_UCM.prmtop" loaded as "CDP". > PyMOL>load ../Cdp_UCM.rst7, CDP, 1, rst > CmdLoad-Error: must load object topology before loading restart file! > > > If files have the default extension and I don't need to to specify the > file type, loading works fine: > > PyMOL>load Cdp_UCM.top, CDP, 1 > ObjectMolecule: Attempting to read Amber7 topology file. > CmdLoad: "Cdp_UCM.top" loaded as "CDP". > PyMOL>load Cdp_UCM.rst, CDP, 1 > ObjectMolecule: read coordinates into state 1... > CmdLoad: "Cdp_UCM.rst" appended into object "CDP". > CmdLoad: 1 total states in the object. > > Of course I can work around this by modifying the extensions on my files > before loading, but due to compatibility issues with other scripts I'd > prefer to leave the extensions I've been using heretofore. > > 2. When using the load_traj command is there a way to select which > frames are to be loaded? For example to load only every 10th frame? > > Pawel -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Get your SQL database under version control now! Version control is standard for application code, but databases havent caught up. So what steps can you take to put your SQL databases under version control? Why should you start doing it? Read more to find out. http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
