cannot open chimerax with structureviz (using ChimeraX 1.5 and cytoscape 3.9.1)
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
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
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 correctpath 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
I tried it again - and it worked!
Not clear what changed, I am sure it was you mail :)
thank you very much!
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
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 mailto: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 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/ 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 mailto: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 http://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 http://www.cs.huji.ac.il/~fora
participants (3)
-
Elaine Meng -
Ora Furman-Schueler -
ora.furman-schueler＠mail.huji.ac.il