Hi, 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 compute that. 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 (514).343.6111 #5352
