Isolde can't be installed inside ChimeraX 1.5
Hi ChimeraX, I met an issue when I try to install Isolde inside ChimeraX 1.5. It will stuck there forever. May I ask you if there are any ways to solve this issue? I tried to use website to download the whl file, but it can’t be recongized by ChimeraX. May I ask you for some suggestions if possible? Many thanks in advance and have a nice day! Best regards, Jun Zhang
Hi Jun Zhang, I was waiting for others to answer this question because I'm not the expert on this topic, but my guess is that you need to use ChimeraX version 1.7.1. I'm saying this because when I look at the Toolshed page for ISOLDE, it says that the ISOLDE downloads work with ChimeraX version numbers that start with 1.7: <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 12, 2024, at 12:45 PM, Jun Zhang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX,
I met an issue when I try to install Isolde inside ChimeraX 1.5. It will stuck there forever. May I ask you if there are any ways to solve this issue? I tried to use website to download the whl file, but it can’t be recongized by ChimeraX. May I ask you for some suggestions if possible?
Many thanks in advance and have a nice day!
Best regards, Jun Zhang
Sorry for being slow on this (caught me travelling)... while there *is* an ISOLDE version on the Toolshed for ChimeraX 1.5, I'd definitely recommend updating to 1.7 for a host of reasons. That being said, it's not clear to me why the installation should be hanging, but the most likely culprit is some issue causing the download to time out. One thing you can try is to use your normal web browser to go to https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxclipper and https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde and download the Clipper and ISOLDE packages for your OS and ChimeraX version (if you have a reason why you *have* to stick with ChimeraX 1.5, you'll need to click on the Release History tab and scroll down until you find Clipper 0.19.0 and ISOLDE 1.5). Then in ChimeraX, on the command line type: toolshed install ... then drag-and-drop the ChimeraX_Clipper...whl file from your downloads folder onto the command line and hit return to install it. Do the same for the ChimeraX_ISOLDE...whl file, restart ChimeraX, and you should be ready to go. Best, Tristan On Wed, Mar 13, 2024 at 11:14 PM Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Jun Zhang, I was waiting for others to answer this question because I'm not the expert on this topic, but my guess is that you need to use ChimeraX version 1.7.1.
I'm saying this because when I look at the Toolshed page for ISOLDE, it says that the ISOLDE downloads work with ChimeraX version numbers that start with 1.7:
<https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 12, 2024, at 12:45 PM, Jun Zhang via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX,
I met an issue when I try to install Isolde inside ChimeraX 1.5. It will stuck there forever. May I ask you if there are any ways to solve this issue? I tried to use website to download the whl file, but it can’t be recongized by ChimeraX. May I ask you for some suggestions if possible?
Many thanks in advance and have a nice day!
Best regards, Jun Zhang
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Hi Tristan, Thank you very much for your kind reply and help! The suggestions are really helpful and it works out for me now！ My Mac can't use 1.7, probably due to the system, so I chose 1.5 as a try. Now, both Clipper and ISOLDE work inside ChimeraX. Many thanks again and have a wonderful rest of the day! Best, Jun Zhang On Wed, Mar 13, 2024 at 7:23 PM Tristan Croll <tcroll@altoslabs.com> wrote:
Sorry for being slow on this (caught me travelling)... while there *is* an ISOLDE version on the Toolshed for ChimeraX 1.5, I'd definitely recommend updating to 1.7 for a host of reasons. That being said, it's not clear to me why the installation should be hanging, but the most likely culprit is some issue causing the download to time out. One thing you can try is to use your normal web browser to go to https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxclipper and https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde and download the Clipper and ISOLDE packages for your OS and ChimeraX version (if you have a reason why you *have* to stick with ChimeraX 1.5, you'll need to click on the Release History tab and scroll down until you find Clipper 0.19.0 and ISOLDE 1.5). Then in ChimeraX, on the command line type:
toolshed install
... then drag-and-drop the ChimeraX_Clipper...whl file from your downloads folder onto the command line and hit return to install it. Do the same for the ChimeraX_ISOLDE...whl file, restart ChimeraX, and you should be ready to go.
Best, Tristan
On Wed, Mar 13, 2024 at 11:14 PM Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Jun Zhang, I was waiting for others to answer this question because I'm not the expert on this topic, but my guess is that you need to use ChimeraX version 1.7.1.
I'm saying this because when I look at the Toolshed page for ISOLDE, it says that the ISOLDE downloads work with ChimeraX version numbers that start with 1.7:
<https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 12, 2024, at 12:45 PM, Jun Zhang via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX,
I met an issue when I try to install Isolde inside ChimeraX 1.5. It will stuck there forever. May I ask you if there are any ways to solve this issue? I tried to use website to download the whl file, but it can’t be recongized by ChimeraX. May I ask you for some suggestions if possible?
Many thanks in advance and have a nice day!
Best regards, Jun Zhang
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (3)
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Elaine Meng -
Jun Zhang -
Tristan Croll