[chimerax-users] [Chimera-users] view MD ChimeraX

[Elaine Meng]

Hi Fabian!
The “Molecular Dynamics Viewer" tool is available on ChimeraX Toolshed from outside developers, i.e. it is not written by our group.  However, the description on Toolshed pretty much says what it does:  it is a simple graphical interface for showing multiframe PDB files as a trajectory.  It doesn’t read other trajectory formats.

<https://cxtoolshed.rbvi.ucsf.edu/apps/moleculardynamicsviewer>

After you install it, it will be under Tools… General in the menu.  Starting the tool from that menu will open a window in ChimeraX and then clicking the Open button in that tool will allow you to browse to and open a multiframe PDB file, like 1PLX.pdb downloaded from the RCSB PDB (NMR structure, so it has multiple conformations each as a MODEL in the single PDB file).  Then you can use the other buttons, e.g. Start to play as a a trajectory.

(I wasn’t sure what you meant by “not able to use it.”)

However, *without* this tool:
Just using ChimeraX without installing anything extra, you can read in a few trajectory formats and then play them with the “coordset” command or using a slider interface shown with “coordset slider".  The trajectory formats known to ChimeraX are listed here:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>
<http://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html>

See also “coordset” and “coordset slider”
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider>

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

P.S. There is also a chimerax-users at cgl.ucsf.edu mailing list, CC’d here.

> On Dec 15, 2019, at 1:50 AM, Fabian Glaser <fglaser at technion.ac.il> wrote:
> 
> Hi,
> I installed Molecular Dynamics Viewer in ChimeraX but I am not able to use it, . I use it successfully in Chimera (no X). But in ChimeraX. 
> Can you please help me?
> Best,
> Fabian