Hi pymol users,
I would like to read a CHARMM generated dcd file which has 200 frames in
it. Is there a way where I can upload dcd and know the rmsd of each residue
in the protein over 200 frames.
What do I have to do to switch off the graphics to speed up the process.
I would appreciate if someone could take some time out to explain the steps
I should do to read a dcd file and find out the RMSD of the residues of the
From: Thomas Holder <speleo3@us...> - 2012-05-07 18:57:28
> I would like to read a CHARMM generated dcd file which has 200 frames in
PyMOL can read DCD files with the "load_traj" command if it has been
compiled with VMD plugins enabled.
An alternative python only implementation is available with the "psico"
module as "load_traj_dcd" (http://pymolwiki.org/index.php/Psico).
> Is there a way where I can upload dcd and know the rmsd of each
> residue in the protein over 200 frames.
Calculating RMSD for each residue separatly is possible, but requires
some scripting. You need the "rms_cur" command for that.
> What do I have to do to switch off the graphics to speed up the process.
You can run PyMOL in "batch mode" with "pymol -cr script.py".
> I would appreciate if someone could take some time out to explain the
> steps I should do to read a dcd file and find out the RMSD of the
> residues of the protein only.
For a protein with 100 residues, the script should look similar to this:
cmd.load_traj_dcd('trajectory.dcd', 'mol', 1)
for state in range(1, cmd.count_states()+1):
for resi in range(2, 100):
sele = 'resi %d' % (resi)
rmsd = cmd.rms_cur(sele, sele, 1, state)
print 'State=%d Residue=%d RMSD=%f' % (state, resi, rmsd)
Hope that helps.
MPI for Developmental Biology
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