I remember this posting from a while ago:

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/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 <jason.vertrees@gmail.com> 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 <nicolasbock@gmail.com> 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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