Re: [PyMOL] Trajectory Movie

[Jason V. <jas...@sc...>]

Hi Lisa,

Load your 88 objects into one multi-state object then intrafit them to
a given selection.  It'll look something like,

# load the PDBs into one object
import glob
for x in glob.glob("/path/to/yourPDBs/*.pdb"):
  cmd.load(x, "obj")

# select your hinge region
cmd.select( "hinge", "i. A-B")
intra_fit hinge
mplay

To be clear: states do store atom positions, frames do not.

Cheers,

-- Jason



On Fri, Jul 16, 2010 at 1:57 PM, YunHui Lisa Lin <li...@pr...> wrote:
> Hello PyMOLers,
>
> I'm trying to make a movie showing the conformational changes of a protein. I'd like to use the "super" command to align conformations in between adjacent frames.
> So far I've written a script that loads one conformation at a time, performs the alignment, disables all other conformations, then stores the present view as a "scene" and sets the corresponding movie frame to that scene. PyMOL keeps crashing on me, and I suspect this is because I'm trying to load a total of 88 objects. If I simply load the PDB files as "states" into a movie, it works fine. However, states do not store object positions, so I'm unable to perform an alignment between frames.
> Does anyone have suggestions how to best approach this?
>
> Thanks in advance,
> Lisa
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120