[chimerax-users] ProblemI am attempting he installation of ChmimeraX Installing ChimeraX on Debian mv-10

Fri Oct 8 13:10:34 PDT 2021

The ChimeraX download page says to install using

sudo apt-get install ~/Downloads/ucsf-chimerax_1.2.5-1_amd64.deb

So it might be worth trying that instead of what you tried "sudo dpkg -i ucsf-chimerax_1.2.5-1_amd64.deb".

	Tom

> On Oct 8, 2021, at 12:59 PM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Stephen, 
> 
> Ok, sorry I don't use Linux much so I don't know why the package manager won't install those dependencies.  Our Linux expert Greg is back from vacation next Wednesday and would have suggestions I am sure.  But in the meantime the mailing list message I linked to suggested a fix to a reported Qt xcb load problem that involved installing some missing package and you could try what it suggests.  I know Greg strongly discourages using the "generic Linux" ChimeraX distribution because this kind of missing library problem you describe is common since Linux distros vary so much in what system libraries they include.
> 
> 	Tom
> 
> 
>> On Oct 8, 2021, at 12:50 PM, Stephen P. Molnar via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> 
>> That was a quick reply. Many thanks.
>> 
>> However:
>> 
>> comp at AbNormal:~/Downloads/ChimeraX$ sudo dpkg -i ucsf-chimerax_1.2.5-1_amd64.deb
>> Selecting previously unselected package ucsf-chimerax.
>> (Reading database ... 509458 files and directories currently installed.)
>> Preparing to unpack ucsf-chimerax_1.2.5-1_amd64.deb ...
>> Unpacking ucsf-chimerax (1.2.5-1) ...
>> dpkg: dependency problems prevent configuration of ucsf-chimerax:
>> ï¿½ucsf-chimerax depends on libgfortran3; however:
>> ï¿½ Package libgfortran3 is not installed.
>> ï¿½ucsf-chimerax depends on libllvm3.8; however:
>> ï¿½ Package libllvm3.8 is not installed.
>> ï¿½ucsf-chimerax depends on libssl1.0.0; however:
>> ï¿½ Package libssl1.0.0 is not installed.
>> 
>> dpkg: error processing package ucsf-chimerax (--install):
>> ï¿½dependency problems - leaving unconfigured
>> Processing triggers for man-db (2.8.5-2) ...
>> Errors were encountered while processing:
>> ï¿½ucsf-chimerax
>> 
>> 
>> 
>> On 10/08/2021 03:22 PM, Tom Goddard wrote:
>>> Hi Stephen,
>>> 
>>> ï¿½ Our linux ChimeraX expert is on vacation but here is an idea. ï¿½The problem is that the Qt window toolkit can't start and that is almost surely a missing system library, probably one that the Qt xcb plugin shared library needs. ï¿½I see a ChimeraX mailing list discussion of this problem here
>>> 
>>> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002339.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002339.html>
>>> 
>>> Supposedly the ChimeraX 1.2.5-1 builds on the download page solved that issue. ï¿½If you are using the "generic Linux" ChimeraX distribution I'd suggest instead using the Ubuntu 18.04 ChimeraX version which is a .deb file for debian 10 according to the ChimeraX download page. ï¿½The advantage of using the .deb distribution is that it uses the Debian package manager to assure the needed libraries are installed, while the "generic Linux" ChimeraX .tar.gz file tries to include ï¿½the needed libraries but not always successfully since different linux distros include different system libraries.
>>> 
>>> 	Tom
>>> 
>>> 
>>> 
>>> 
>>>> On Oct 8, 2021, at 12:04 PM, Stephen P. Molnar via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>>> 
>>>> I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I ï¿½open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following:
>>>> 
>>>> comp at AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ <mailto:comp at AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$> ./ChimeraX
>>>> qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
>>>> This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
>>>> 
>>>> Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb.
>>>> 
>>>> Fatal Python error: Aborted
>>>> 
>>>> Current thread 0x00007fcb3dafd740 (most recent call first):
>>>> ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__
>>>> ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init
>>>> ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module>
>>>> ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code
>>>> ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main
>>>> Aborted
>>>> comp at AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ <mailto:comp at AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$>
>>>> 
>>>> xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem?
>>>> 
>>>> Is there a solution? Reinstalling did not fix the problem.
>>>> 
>>>> Thanks in advance.
>>>> 
>>>> -- 
>>>> Stephen P. Molnar, Ph.D.
>>>> www.molecular-modeling.net <http://www.molecular-modeling.net/>
>>>> 614.312.7528 (c)
>>>> Skype: ï¿½smolnar1
>>>> 
>>>> _______________________________________________
>>>> ChimeraX-users mailing list
>>>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>>>> Manage subscription:
>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
>>>> 
>>> 
>> 
>> -- 
>> Stephen P. Molnar, Ph.D.
>> www.molecular-modeling.net <http://www.molecular-modeling.net/>
>> 614.312.7528 (c)
>> Skype:  smolnar1
>> 
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211008/3dd49f36/attachment.html>