On 7 May 2023, at 19:32, Ora Furman-Schueler <ora.furman-schueler@mail.huji.ac.il> wrote:

I tried that too. Did not work either.

Chimera is in my applications folder. I changed the path in the structurevis app accordingly. I will try again

Ora

On Sun, May 7, 2023, 7:14 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Dear Ora,
ChimeraX and Chimera are two different programs.  StructureViz2 works with Chimera, not ChimeraX.

<https://www.rbvi.ucsf.edu/cytoscape/structureViz2/index.shtml>

Launching Chimera from Cytoscape using structureViz2 works for me.  I have it set up to use the Chimera.app on my desktop, with path:

/Users/meng/Desktop/Chimera.app/Contents/MacOS/chimera

What tutorial are you viewing?  Does it say to use ChimeraX?  Presumably you need to use UCSF Chimera instead, and also include the full path as in the example above (with /chimera) on the end.

Chimera website (download, etc.)
<https://www.rbvi.ucsf.edu/chimera/>

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

> On May 6, 2023, at 8:05 AM, ora.furman-schueler--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear Support team
>
> We are teaching a network course and would like to show an example of analysis of proteins as networks. I have tried to follow the structureviz2 tutorial but I cannot get past the very first step of linking ChimeraX to cytoscape.
>
> I did define the Chimera location path
> /Applications/ChimeraX-1.5.app/Contents/MacOS
>
> What am I doing wrong?
>
> This is the error message that I get in cytocape.
>
>
>        Launching Chimera
>       •  Launching Chimera ...
>       •  UCSF Chimera could not be launched. Make sure that the correct path to Chimera is set in structureViz -> Settings…
>
>
> thank you for your help!
>
> Ora
>
> Prof. Ora Schueler-Furman
> Dept. of Microbiology and Molecular Genetics, IMRIC
> Jacob Epstein Chair in Bacteriology
> Hebrew University, Hadassah Medical School
> POB 12272, Jerusalem
> 91120 Israel
> Tel:   972-2-675-7094
> FAX: 972-2-675-7308
> Furman lab site: www.cs.huji.ac.il/~fora