Re: [PyMOL] Fwd: loading amber files and selecting traj frames

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