Sorry Viktor and Warren, but I don't think your suggestions are
applicable. I have only a single protein molecule in my trajectory,
which I kept centered at the origin, so it never traverses the
periodic boundary. I did strip all but 20 waters from it using ptraj
and created the appropriate
Dmitry,
is your system a single molecule or is it composed of multiple molecules
(e.g. dimer)? Amber should not 'cut' your molecule into pieces, imaging
can only separate molecules in a dimer, trimer or such. Also, was your
system solvated? Did you strip water before visualizing in PyMOL? The
...@delsci.com
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Dmitry Kondrashov
> Sent: Saturday, November 19, 2005 9:57 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMO
Hi,
I have a prloblem with viewing AMBER trajectory files, specifically,
the topology appears messed up. When I load the trajectory into the
topology object, the structure shows up dismembered into eight pieces
on the vertices of a cude. I should note that I can load an AMBER
coordinate f
