Hi Francois, I'm told that although ChimeraX itself does not read XYZ files, you can add that capability by installing the SeqCrow plugin. ChimeraX menu: Tools... More Tools wil show the Toolshed website in the ChimeraX browser, in which you can find SeqCrow and install if it you like. Here is the URL where you can see information about SeqCrow, but to install, it is more convenient to use the ChimeraX menu and browser as mentioned above. <https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 6, 2023, at 9:40 PM, Francois Berenger via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Apparently, chimerax cannot even open a single-molecule .xyz file ?!

---------- Forwarded message --------- From: Francois Berenger <berenger@edu.k.u-tokyo.ac.jp> Date: Fri, Apr 7, 2023 at 1:09 PM Subject: Chimera cannot read multi-molecules .xyz files in To: <chimera-users@cgl.ucsf.edu>

Dear list,

I can read one molecule fine in .xyz format using chimera.

However, if my .xyz file has several molecules (like a MD trajectory), chimera fails to read it in.

Is there planned support for MD trajectories given as .xyz file?

I have chimera-1.16. I shall test with ChimeraX very soon.

Regards, F.

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It would be nice if a multiple-molecule file can be read as a (coordinates only) MD trajectory. On Sat, Apr 8, 2023 at 2:21 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Francois, There is no formal XYZ file format definition. Chimera reads the format as described in Wikipedia <https://en.wikipedia.org/wiki/XYZ_file_format>, which only allows for one molecule per file.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

On Apr 6, 2023, at 9:09 PM, Francois Berenger via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:

Dear list,

I can read one molecule fine in .xyz format using chimera.

However, if my .xyz file has several molecules (like a MD trajectory), chimera fails to read it in.

Is there planned support for MD trajectories given as .xyz file?

I have chimera-1.16. I shall test with ChimeraX very soon.

Regards, F.

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users