Isolde installation in chimeraX
Hi,
I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara
Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara
Hi Elaine, I did that. I clicked on the install in the toolshed, but all it does is download the bundle. Is there a way to manually install it? Chiara
From: Elaine Meng meng@cgl.ucsf.edu Date: Tuesday, 13 June 2023 at 11:21 To: Chiara Rapisarda aglape@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Isolde installation in chimeraX Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara
Did you open the Toolshed from the ChimeraX menu as suggested? It is different if you just open it in a different web browser instead of from inside ChimeraX. If you open it from the ChimeraX menu, it will tell you if the versions are compatible.
Secondly, did you get any error messages or feedback of any kind?
But yes, you can install it manually, but I suspect there is some problem if the suggested method did not work. For manual installation, see command "toolshed install" for specifying a filename directly. Again, if the recommended method didn't work, this may not work either, e.g. if not compatible with your version or other problem.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/toolshed.html#install
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 8:23 AM, Chiara Rapisarda via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, I did that. I clicked on the install in the toolshed, but all it does is download the bundle. Is there a way to manually install it? Chiara
From: Elaine Meng meng@cgl.ucsf.edu Date: Tuesday, 13 June 2023 at 11:21 To: Chiara Rapisarda aglape@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Isolde installation in chimeraX
Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi,
I have included a screen shot. If it was the version it would give me an error. It tells me that the budle is downloaded, but the installation doesn’t work as I cannot see Isolde in the general tools. Any ideas? Best, Chiara
From: Elaine Meng meng@cgl.ucsf.edu Date: Tuesday, 13 June 2023 at 11:33 To: Chiara Rapisarda <aglape@gmail.co[A screenshot of a computer Description automatically generated with medium confidence]m> Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Isolde installation in chimeraX Did you open the Toolshed from the ChimeraX menu as suggested? It is different if you just open it in a different web browser instead of from inside ChimeraX. If you open it from the ChimeraX menu, it will tell you if the versions are compatible.
Secondly, did you get any error messages or feedback of any kind?
But yes, you can install it manually, but I suspect there is some problem if the suggested method did not work. For manual installation, see command "toolshed install" for specifying a filename directly. Again, if the recommended method didn't work, this may not work either, e.g. if not compatible with your version or other problem.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/toolshed.html#install
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 8:23 AM, Chiara Rapisarda via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, I did that. I clicked on the install in the toolshed, but all it does is download the bundle. Is there a way to manually install it? Chiara
From: Elaine Meng meng@cgl.ucsf.edu Date: Tuesday, 13 June 2023 at 11:21 To: Chiara Rapisarda aglape@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Isolde installation in chimeraX
Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi Chiara,
I’m not at my computer right now so I can’t check for sure, but I think the issue might be that you need to update your ChimeraX to the official 1.6.1 release. I can’t remember off the top of my head exactly which ChimeraX release candidate I built the ISOLDE release against, but I’m pretty sure it was later than that one.
Best, Tristan
On Tue, 13 Jun 2023 at 17:08, Chiara Rapisarda via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I have included a screen shot. If it was the version it would give me an error. It tells me that the budle is downloaded, but the installation doesn’t work as I cannot see Isolde in the general tools.
Any ideas?
Best,
Chiara
*From: *Elaine Meng meng@cgl.ucsf.edu *Date: *Tuesday, 13 June 2023 at 11:33 *To: *Chiara Rapisarda <aglape@gmail.co[image: A screenshot of a computer Description automatically generated with medium confidence]m> *Cc: *ChimeraX Users Help chimerax-users@cgl.ucsf.edu *Subject: *Re: [chimerax-users] Isolde installation in chimeraX
Did you open the Toolshed from the ChimeraX menu as suggested? It is different if you just open it in a different web browser instead of from inside ChimeraX. If you open it from the ChimeraX menu, it will tell you if the versions are compatible.
Secondly, did you get any error messages or feedback of any kind?
But yes, you can install it manually, but I suspect there is some problem if the suggested method did not work. For manual installation, see command "toolshed install" for specifying a filename directly. Again, if the recommended method didn't work, this may not work either, e.g. if not compatible with your version or other problem.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/toolshed.html#install
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 8:23 AM, Chiara Rapisarda via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, I did that. I clicked on the install in the toolshed, but all it does is
download the bundle.
Is there a way to manually install it? Chiara
From: Elaine Meng meng@cgl.ucsf.edu Date: Tuesday, 13 June 2023 at 11:21 To: Chiara Rapisarda aglape@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Isolde installation in chimeraX
Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in
that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download
the bundle, but nothing happens afterwards.
Can you help me find out what is wrong? Thanks, Chiara
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Tristan is right. If you click on the "Release History" tab of ISOLDE's Toolshed page, you can see that your release candidate is older than earliest release candidates that ISOLDE 1.6 works with. So if you update to Chimera 1.6.1 then things should work.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 13, 2023, at 9:12 AM, Tristan Croll via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Chiara,
I’m not at my computer right now so I can’t check for sure, but I think the issue might be that you need to update your ChimeraX to the official 1.6.1 release. I can’t remember off the top of my head exactly which ChimeraX release candidate I built the ISOLDE release against, but I’m pretty sure it was later than that one.
Best, Tristan
On Tue, 13 Jun 2023 at 17:08, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: Hi,
I have included a screen shot. If it was the version it would give me an error. It tells me that the budle is downloaded, but the installation doesn’t work as I cannot see Isolde in the general tools.
Any ideas?
Best,
Chiara
From: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Date: Tuesday, 13 June 2023 at 11:33 To: Chiara Rapisarda <aglape@gmail.co mailto:aglape@gmail.co<image001.png>m> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Isolde installation in chimeraX
Did you open the Toolshed from the ChimeraX menu as suggested? It is different if you just open it in a different web browser instead of from inside ChimeraX. If you open it from the ChimeraX menu, it will tell you if the versions are compatible.
Secondly, did you get any error messages or feedback of any kind?
But yes, you can install it manually, but I suspect there is some problem if the suggested method did not work. For manual installation, see command "toolshed install" for specifying a filename directly. Again, if the recommended method didn't work, this may not work either, e.g. if not compatible with your version or other problem.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/toolshed.html#install https://rbvi.ucsf.edu/chimerax/docs/user/commands/toolshed.html#install>
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 8:23 AM, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, I did that. I clicked on the install in the toolshed, but all it does is download the bundle. Is there a way to manually install it? Chiara
From: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Date: Tuesday, 13 June 2023 at 11:21 To: Chiara Rapisarda <aglape@gmail.com mailto:aglape@gmail.com> Cc: chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Isolde installation in chimeraX
Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Manage subscription:
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Manage subscription: _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
I am downloading the nightly build. I saw that the official release is 1 month before the range of compatibility…. I was wondering if it was our security system, and got no error message, so I didn’t know whether it was us or chimera. Let’s hope it’s the version…
From: Tristan Croll tcroll@altoslabs.com Date: Tuesday, 13 June 2023 at 12:12 To: Chiara Rapisarda aglape@gmail.com Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Re: Isolde installation in chimeraX Hi Chiara,
I’m not at my computer right now so I can’t check for sure, but I think the issue might be that you need to update your ChimeraX to the official 1.6.1 release. I can’t remember off the top of my head exactly which ChimeraX release candidate I built the ISOLDE release against, but I’m pretty sure it was later than that one.
Best, Tristan
On Tue, 13 Jun 2023 at 17:08, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote: Hi,
I have included a screen shot. If it was the version it would give me an error. It tells me that the budle is downloaded, but the installation doesn’t work as I cannot see Isolde in the general tools. Any ideas? Best, Chiara
From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Date: Tuesday, 13 June 2023 at 11:33 To: Chiara Rapisarda <aglape@gmail.comailto:aglape@gmail.co[A screenshot of a computer Description automatically generated with medium confidence]m> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Isolde installation in chimeraX Did you open the Toolshed from the ChimeraX menu as suggested? It is different if you just open it in a different web browser instead of from inside ChimeraX. If you open it from the ChimeraX menu, it will tell you if the versions are compatible.
Secondly, did you get any error messages or feedback of any kind?
But yes, you can install it manually, but I suspect there is some problem if the suggested method did not work. For manual installation, see command "toolshed install" for specifying a filename directly. Again, if the recommended method didn't work, this may not work either, e.g. if not compatible with your version or other problem.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/toolshed.html#install
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 8:23 AM, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, I did that. I clicked on the install in the toolshed, but all it does is download the bundle. Is there a way to manually install it? Chiara
From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Date: Tuesday, 13 June 2023 at 11:21 To: Chiara Rapisarda <aglape@gmail.commailto:aglape@gmail.com> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Isolde installation in chimeraX
Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Manage subscription:
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi Chiara,
The current ISOLDE release won’t install in the current daily builds - those are now versioned 1.7.dev{XXX} and have (amongst other things) changed the Python version they use. You really want the 1.6.1 *release* for the time being.
Best, Tristan
On Tue, 13 Jun 2023 at 17:17, Chiara Rapisarda aglape@gmail.com wrote:
I am downloading the nightly build. I saw that the official release is 1 month before the range of compatibility….
I was wondering if it was our security system, and got no error message, so I didn’t know whether it was us or chimera.
Let’s hope it’s the version…
*From: *Tristan Croll tcroll@altoslabs.com *Date: *Tuesday, 13 June 2023 at 12:12 *To: *Chiara Rapisarda aglape@gmail.com *Cc: *ChimeraX Users Help chimerax-users@cgl.ucsf.edu *Subject: *Re: [chimerax-users] Re: Isolde installation in chimeraX
Hi Chiara,
I’m not at my computer right now so I can’t check for sure, but I think the issue might be that you need to update your ChimeraX to the official 1.6.1 release. I can’t remember off the top of my head exactly which ChimeraX release candidate I built the ISOLDE release against, but I’m pretty sure it was later than that one.
Best,
Tristan
On Tue, 13 Jun 2023 at 17:08, Chiara Rapisarda via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I have included a screen shot. If it was the version it would give me an error. It tells me that the budle is downloaded, but the installation doesn’t work as I cannot see Isolde in the general tools.
Any ideas?
Best,
Chiara
*From: *Elaine Meng meng@cgl.ucsf.edu *Date: *Tuesday, 13 June 2023 at 11:33 *To: *Chiara Rapisarda <aglape@gmail.co[image: A screenshot of a computer Description automatically generated with medium confidence]m> *Cc: *ChimeraX Users Help chimerax-users@cgl.ucsf.edu *Subject: *Re: [chimerax-users] Isolde installation in chimeraX
Did you open the Toolshed from the ChimeraX menu as suggested? It is different if you just open it in a different web browser instead of from inside ChimeraX. If you open it from the ChimeraX menu, it will tell you if the versions are compatible.
Secondly, did you get any error messages or feedback of any kind?
But yes, you can install it manually, but I suspect there is some problem if the suggested method did not work. For manual installation, see command "toolshed install" for specifying a filename directly. Again, if the recommended method didn't work, this may not work either, e.g. if not compatible with your version or other problem.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/toolshed.html#install
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 8:23 AM, Chiara Rapisarda via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, I did that. I clicked on the install in the toolshed, but all it does is
download the bundle.
Is there a way to manually install it? Chiara
From: Elaine Meng meng@cgl.ucsf.edu Date: Tuesday, 13 June 2023 at 11:21 To: Chiara Rapisarda aglape@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Isolde installation in chimeraX
Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in
that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download
the bundle, but nothing happens afterwards.
Can you help me find out what is wrong? Thanks, Chiara
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Indeed the 1.6.1 worked, it was very easy. Thanks for the help From: Tristan Croll tcroll@altoslabs.com Date: Tuesday, 13 June 2023 at 12:21 To: Chiara Rapisarda aglape@gmail.com Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Re: Isolde installation in chimeraX Hi Chiara,
The current ISOLDE release won’t install in the current daily builds - those are now versioned 1.7.devhttp://1.7.dev{XXX} and have (amongst other things) changed the Python version they use. You really want the 1.6.1 *release* for the time being.
Best, Tristan
On Tue, 13 Jun 2023 at 17:17, Chiara Rapisarda <aglape@gmail.commailto:aglape@gmail.com> wrote: I am downloading the nightly build. I saw that the official release is 1 month before the range of compatibility…. I was wondering if it was our security system, and got no error message, so I didn’t know whether it was us or chimera. Let’s hope it’s the version…
From: Tristan Croll <tcroll@altoslabs.commailto:tcroll@altoslabs.com> Date: Tuesday, 13 June 2023 at 12:12 To: Chiara Rapisarda <aglape@gmail.commailto:aglape@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Re: Isolde installation in chimeraX Hi Chiara,
I’m not at my computer right now so I can’t check for sure, but I think the issue might be that you need to update your ChimeraX to the official 1.6.1 release. I can’t remember off the top of my head exactly which ChimeraX release candidate I built the ISOLDE release against, but I’m pretty sure it was later than that one.
Best, Tristan
On Tue, 13 Jun 2023 at 17:08, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote: Hi,
I have included a screen shot. If it was the version it would give me an error. It tells me that the budle is downloaded, but the installation doesn’t work as I cannot see Isolde in the general tools. Any ideas? Best, Chiara
From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Date: Tuesday, 13 June 2023 at 11:33 To: Chiara Rapisarda <aglape@gmail.comailto:aglape@gmail.co[A screenshot of a computer Description automatically generated with medium confidence]m> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Isolde installation in chimeraX Did you open the Toolshed from the ChimeraX menu as suggested? It is different if you just open it in a different web browser instead of from inside ChimeraX. If you open it from the ChimeraX menu, it will tell you if the versions are compatible.
Secondly, did you get any error messages or feedback of any kind?
But yes, you can install it manually, but I suspect there is some problem if the suggested method did not work. For manual installation, see command "toolshed install" for specifying a filename directly. Again, if the recommended method didn't work, this may not work either, e.g. if not compatible with your version or other problem.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/toolshed.html#install
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 8:23 AM, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, I did that. I clicked on the install in the toolshed, but all it does is download the bundle. Is there a way to manually install it? Chiara
From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Date: Tuesday, 13 June 2023 at 11:21 To: Chiara Rapisarda <aglape@gmail.commailto:aglape@gmail.com> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Isolde installation in chimeraX
Hi Chiara, The easiest way to install Toolshed bundles is from inside ChimeraX: in that case, it should just be a single click to download/install, if it is available for your version of ChimeraX. Start ChimeraX, choose menu: Tools... More Tools, and in the Toolshed, click to choose the ISOLDE app. In the resulting page, there should either be an Install button or a message saying it is not available for the version of ChimeraX that you are using. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 13, 2023, at 3:28 AM, Chiara Rapisarda via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Manage subscription:
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Manage subscription:
participants (4)
-
Chiara Rapisarda -
Elaine Meng -
Eric Pettersen -
Tristan Croll