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
>
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