I had to change the trajectory into .mdcrd and took the take care of the box I
believe. I am not sure you can keep .nc format without the truncated octahedron
tbf.
Thank you!
Lenka
________________________________
From: Mateusz Bieniek <bieniek...@gmail.com>
Sent: 23 July 2018 14:28:12
To: Stejskal, Lenka
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Amber .nc
Can you share what error/message you get when you try to load the trajectory
with the command?
The snippet of code I shared works for me. According to this page it should
just work: https://pymolwiki.org/index.php/Load_Traj
Load Traj - PyMOLWiki<https://pymolwiki.org/index.php/Load_Traj>
pymolwiki.org
load_traj loads a trajectory as "states" into an already loaded molecular
object.. Since version 1.0, PyMOL uses the Molfile Plugin backend, which
supports a variety of trajectory file formats.
Do you happen to use a truncated octahedron?
Best, Mat
On Mon, Jul 23, 2018 at 2:27 PM Stejskal, Lenka
<lenka.stejskal...@ucl.ac.uk<mailto:lenka.stejskal...@ucl.ac.uk>> wrote:
Hi Mat,
I have of course read that but I am still unable to load the trajectory. I was
looking for an actual successful example not just a guide.
Thanks
Lenka
________________________________
From: Mateusz Bieniek <bieniek...@gmail.com<mailto:bieniek...@gmail.com>>
Sent: 23 July 2018 14:04:22
To: Stejskal, Lenka
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] Amber .nc
Hi Lenka,
Let me first state that the command "help load_traj" points to the webpage
which in turns says that the .nc format is supported by pymol.
I come from the gromacs background. Once you load the topology/state of your
system (in my case .gro or .pdb), then use "load_traj", ie
load_traj trajectory.nc<http://trajectory.nc>
There are other options for this command (start, end, shift, etc).
Hope this helps, Mat
On Mon, Jul 23, 2018 at 11:42 AM Stejskal, Lenka
<lenka.stejskal...@ucl.ac.uk<mailto:lenka.stejskal...@ucl.ac.uk>> wrote:
Dear Pymol users,
Can somebody advise how I can open amber trajectory file in .nc format?
Thank you
Lenka
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