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
> -----Original Message-----
> From: Guilherme Menegon Arantes [mailto:garan...@iq.usp.br]
> Sent: Wednesday, April 29, 2009 6:44 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] form and break bonds in movie
>
>
> Hi there,
>
> I would like to produce a movie where bonds break and form. However,
> when I load the .pdb files in PyMOL, the bond status (formed or broken)
> stays the same as seen for the first state, even if the bond
> lenghts change considerably.
>
> Any tips on how to do this are welcome. I have goggled and searched the
> archives, but found nothing.
>
> Greetings,
>
> G
>
> --
>
> Guilherme Menegon Arantes, PhD São Paulo, Brasil
> ______________________________________________________
>
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and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
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