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 <[email protected]> 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) [email protected]
(o) +1 (603) 374-7120
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