I'm using pymol to analyse a molecular dynamic simulation.
I transformed my trajectory in an NMR style .pdb.
It's really nice like that: I can see a movie of my simulation in pymol.
Here come my question.
I use intra_fit to align all my frames (states). And it's really fast to
Is there a way to output the rmsd in a file ?
I can see it the GUI but I would like it in a text file.
cmd.intra_fit: 0.008 in state 1 vs state 1
cmd.intra_fit: 0.014 in state 2 vs state 1
cmd.intra_fit: 0.010 in state 101 vs state 1
Same thing for a distance.
Is there a way to make a python script that can
1) load my pdb
2) use one or several pymol commands
3) output the results in a file
Mathieu Coincon PhD Student
Universite De Montreal/Departement de biochimie
Pavillon Roger Gaudry Local D345