I remember this posting from a while ago:
http://www.mail-archive.com/[email protected]/msg06885.html
which may have some clues.
--- begin ---
Whoops, my bad -- I duped the approval before seeing your repost!
Answer:
# first create a phony molecular trajectory
load $PYMOL_PATH/test/dat/pept.pdb, obj
for a in range(2,31): cmd.create("obj","obj",1,a)
unbond 5/c, 6/n
protect not ((5/c or 6/n) extend 4)
sculpt_activate obj, 30
sculpt_iterate obj, 30, 100
smooth obj, 30, 3
# then program a bond-break/re-form movie
mset 1 x30 1 -30 30 x30 30 -1
mdo 45: unbond 5/c, 6/n, quiet=1
mdo 100: bond 5/c, 6/n, quiet=1
frame 100
as sticks
orient 5-6/n+ca+c
mplay
# NOTE: only tested on PyMOL 1.2.x
Cheers,
warren
---- end ----
On Mon, Dec 14, 2009 at 1:12 PM, Jason Vertrees <[email protected]>wrote:
> Nick,
>
> Interesting question. My best guess at this point is that PyMOL can't
> do what you want. You can load the XYZ file into multiple distinct
> objects:
>
> load myXYZ.xyz, multiplex=1
>
> and each object will be shown with proper bonding. However, the
> moment you try to combine those into one structure they retain the
> bonding topology of the first structure. If you change any
> intermediate state, then they all change.
>
> Anyone else?
>
> -- Jason
>
> --
> Jason Vertrees, PhD
>
> PyMOLWiki -- http://www.pymolwiki.org
>
>
>
> On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock <[email protected]>
> wrote:
> > Hello list,
> >
> > I have a bunch of xyz files that are along a transition path in a
> molecule.
> > When I load all of them into pymol and step through the individual
> frames,
> > pymol calculates the bonds only for the initial frame. This leads to
> wrong
> > bonding in subsequent frames since some atoms move quite a bit during the
> > transition. How can I get "dynamic" bonding so that bonding is
> recalculated
> > for each frame?
> >
> > nick
> >
> >
> >
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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