pymol-users

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

[Pawel <pa...@gm...>]

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

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

[Thomas H. <tho...@sc...>]

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

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

[Thomas H. <tho...@sc...>]

Hi Pawel and everybody,

> 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:

yesterday I made some improvements to crd/rst loading and pushed it to
sourceforge SVN. Quick summary:

 - rst and rst7 are recognized as amber restart files. Such files have
   a two-line header and exactly one coordinate set (no trajectory)
   formatted as 6 columns of 12.7 floating point numbers.
   http://ambermd.org/formats.html#restart

 - crd is recognized as amber trajectory file. Such files have a
   one-line header and any number of coordinate sets, formatted as 10
   columns of 8.3 floating point numbers. PyMOL assumes there is no box.
   http://ambermd.org/formats.html#trajectory

Both formats can be loaded with "load", not with "load_traj".

Cheers,
  Thomas

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

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

[Pawel <pa...@gm...>]

Hi Thomas,

Thanks for taking the time to add this. If I may suggest two things:

1. It might also be nice to add support for both "top" and "prmtop" 
extension to be recognized as an amber topology file by the load 
command. Many people in the Amber community are now using "prmtop" as 
the default extension.

2. For the future in might be nice to add support for loading Amber 
trajectories written in netcdf format (".nc" extension). This is quickly 
becoming the default for saving trajectories as it occupies roughly half 
the disk space as traditional "crd" trajectories.

Pawel


On 08/01/2013 03:13 AM, Thomas Holder wrote:
> Hi Pawel and everybody,
>
>> 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:
> yesterday I made some improvements to crd/rst loading and pushed it to
> sourceforge SVN. Quick summary:
>
>   - rst and rst7 are recognized as amber restart files. Such files have
>     a two-line header and exactly one coordinate set (no trajectory)
>     formatted as 6 columns of 12.7 floating point numbers.
>     http://ambermd.org/formats.html#restart
>
>   - crd is recognized as amber trajectory file. Such files have a
>     one-line header and any number of coordinate sets, formatted as 10
>     columns of 8.3 floating point numbers. PyMOL assumes there is no box.
>     http://ambermd.org/formats.html#trajectory
>
> Both formats can be loaded with "load", not with "load_traj".
>
> Cheers,
>    Thomas
>