Hi Jason,
thanks for the hint. That works just fine.
nick
On Mon, Dec 14, 2009 at 11:12, Jason Vertrees 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.x
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_PA
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 stru
Hi Jason,
sure, I have attached the xyz file to this email. We print out forces in
columns 4-6 in the xyz. I run
PyMOL(TM) Molecular Graphics System, Version 1.2r1.
on linux, 64-bit. Let me know if you need any additional information.
Thanks, nick
On Mon, Dec 14, 2009 at 10:20, Jason Vertrees
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 b
