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