Andrea,
I use MD quite a lot myself and we have some "in-house" tools that perform this
function (converting a set of PDB files into a trajectory). However, I took it
upon myself as a challenge to see if I could implement this into PyMOL as a
Python script. Thus, last night I worked feverishly and created a script (now
posted on the PyMOL-Wiki) called "save2traj".
Do the following:
1) Save the script from the PyMOL-Wiki page
2) Load a PDB structure (let's assume that this pdb file is called "struct.pdb")
3) Load other states into this same PDB object (let's assume this object is
called "struct")
4) Then, to save the states as a trajectory, use the following command:
run save2traj
save2traj struct, trajectory
The syntax for the command is
save2traj selection, name
The "name" denotes the output file and will automatically have ".dcd" appended
to it. In the future, there will be additional support for other file formats
but that may be in the distant future. As well, please be aware that due to
PyMOL's RESID renumbering that the trajectory being produced will be numbered
differently than your original PDB. There are two ways around this,
1) Save a corresponding PDB file for that trajectory that is renumbered by PyMOL
or
2) Retain the RESID (see PyMOL-Wiki)
Since this was done on a whim, please use at your own risk until it is further
developed. Hope this helps!
Sean Law
Michigan State University
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