[chimerax-users] How do I visualize an amber nc file in ChimeraX?

[Elaine Meng]

Hello Yasmene,
ChimeraX does not yet have as many features for MD trajectory analysis as Chimera's MD Movie tool.  However, ChimeraX can play back trajectories and show a simple slider GUI, which might be all you need.

As for reading this type of trajectory, I am not sure you have the necessary files.  ChimeraX requires two files for a trajectory, the coordinates and the topology.  It can read AMBER netcdf (.nc) for the coordinates, and for the topology you either need a PDB file or a PSF file.  If you think what you have might be a PSF file, you could try naming it something.psf and then opening the two files, e.g. command something like

open myfile.psf coords myfile.nc 

(where you would have to specify the paths to the files if they are not in your working dirrectory).  However, it may not be a PSF file, and trying to do that would just give you a bunch of errors.

Can VMD write a PDB file of a snapshot from the trajectory?    If so, you can use that for the topology.  You would first open the PDB file in ChimeraX, and then open the .nc file, e.g. something like

open myfile.pdb
open myfile.nc structureModel #1

See help for information on opening trajectory files
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 27, 2022, at 7:14 PM, Yasmene Wang Elhady via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello, 
> 
> I'm new to molecular modeling, and new to Chimera.
> I'm trying to visualize an AMBER .nc output file from an AMBER tutorial (http://ambermd.org/tutorials/basic/tutorial0/), and I have a topology file that in VMD is the type AMBER7 Parm. How can I visualize this in ChimeraX?
> 
> I saw another thread suggesting to use the MD movie tool, but I don't see that option in ChimeraX. Is this something I need to add? If so, where can I get it from, and how do I add it?
> 
> Thanks in advance,
> Yasmene