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@cgl.ucsf.edu wrote:

That was a quick reply. Many thanks.

However:

comp@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: �ucsf-chimerax depends on libgfortran3; however: � Package libgfortran3 is not installed. �ucsf-chimerax depends on libllvm3.8; however: � Package libllvm3.8 is not installed. �ucsf-chimerax depends on libssl1.0.0; however: � Package libssl1.0.0 is not installed.

dpkg: error processing package ucsf-chimerax (--install): �dependency problems - leaving unconfigured Processing triggers for man-db (2.8.5-2) ... Errors were encountered while processing: �ucsf-chimerax

On 10/08/2021 03:22 PM, Tom Goddard wrote:

...

Hi Stephen,

� Our linux ChimeraX expert is on vacation but here is an idea. �The 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. �I 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. �If 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. �The 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 �the 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@cgl.ucsf.edu mailto:chimerax-users@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 �open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following:

comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ mailto:comp@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): �File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ �File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init �File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> �File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code �File "/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@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ mailto:comp@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: �smolnar1

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Indeed, using dpkg instead of apt or apt-get is most likely the reason it did not work. This is because in Debian and its derivatives, dpkg is the low-level program with the only task of installing a given (set of) deb package(s) into the system. But dpkg by itself has no dependency resolution mechanism, which is what apt (or apt-get) is doing (and these, if I understand correctly, internally defer all the installation tasks to dpkg once they are done resolving dependencies).

Guillaume

On 8 Oct 2021, at 22:10, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:

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@cgl.ucsf.edumailto:chimerax-users@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@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:

That was a quick reply. Many thanks.

However:

comp@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: �ucsf-chimerax depends on libgfortran3; however: � Package libgfortran3 is not installed. �ucsf-chimerax depends on libllvm3.8; however: � Package libllvm3.8 is not installed. �ucsf-chimerax depends on libssl1.0.0; however: � Package libssl1.0.0 is not installed.

dpkg: error processing package ucsf-chimerax (--install): �dependency problems - leaving unconfigured Processing triggers for man-db (2.8.5-2) ... Errors were encountered while processing: �ucsf-chimerax

On 10/08/2021 03:22 PM, Tom Goddard wrote: Hi Stephen,

� Our linux ChimeraX expert is on vacation but here is an idea. �The 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. �I see a ChimeraX mailing list discussion of this problem here

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. �If 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. �The 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 �the 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@cgl.ucsf.edumailto:chimerax-users@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 �open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following:

comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$mailto:comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./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): �File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ �File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init �File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> �File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code �File "/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@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$mailto:comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$

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.nethttp://www.molecular-modeling.net/ 614.312.7528 (c) Skype: �smolnar1

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

-- Stephen P. Molnar, Ph.D. www.molecular-modeling.nethttp://www.molecular-modeling.net/ 614.312.7528 (c) Skype: smolnar1

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

If you're installing a locally downloaded package with apt-get, you need to provide the path to the file (even if it's in your current working directory), i.e.:

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

-- Tristan ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Stephen P. Molnar via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: 09 October 2021 12:50 To: goddard goddard@sonic.net; ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ProblemI am attempting he installation of ChmimeraX Installing ChimeraX on Debian mv-10

An interesting suggestion, but

comp@AbNormal:~/Downloads/ChimeraX$ sudo apt-get install ucsf-chimerax_1.2.5-1_amd64.deb [sudo] password for comp: Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package ucsf-chimerax_1.2.5-1_amd64.deb E: Couldn't find any package by glob 'ucsf-chimerax_1.2.5-1_amd64.deb' E: Couldn't find any package by regex 'ucsf-chimerax_1.2.5-1_amd64.deb' comp@AbNormal:~/Downloads/ChimeraX$

None of the missing packages are available via Synaptic.

On 10/08/2021 04:10 PM, Tom Goddard wrote: sudo apt-get install ~/Downloads/ucsf-chimerax_1.2.5-1_amd64.deb

-- Stephen P. Molnar, Ph.D. www.molecular-modeling.nethttp://www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

Hi Stephen,

Unfortunately, your version of Linux is not supported by ChimeraX.  However, Ubuntu 18.04 is based on Debian 10, so there's a chance that the deb file for Ubuntu 18.04 will work.  I apologize for the deb file names being the same for every Ubuntu version, I will look into fixing that.  So please go back to the website and get the deb file for Ubuntu 18.04, and try installing it.

-- Greg

On 10/9/2021 5:26 AM, Stephen P. Molnar via ChimeraX-users wrote:

Thanks for your reply.

Here's what happened:

comp@AbNormal:~/Downloads/ChimeraX$ sudo apt-get install ./ucsf-chimerax_1.2.5-1_amd64.deb [sudo] password for comp: Reading package lists... Done Building dependency tree������ Reading state information... Done Note, selecting 'ucsf-chimerax' instead of './ucsf-chimerax_1.2.5-1_amd64.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:

The following packages have unmet dependencies: �ucsf-chimerax : Depends: libgfortran3 but it is not installable ���������������� Depends: libllvm3.8 but it is not installable ���������������� Depends: libssl1.0.0 but it is not installable E: Unable to correct problems, you have held broken packages. comp@AbNormal:~/Downloads/ChimeraX$

Synaptic didn't find any broken packages. Although I've been using Linux since the Red Hat Mother's Day distribution, I am strictly an Organic Chemist. not a computer person.

On 10/09/2021 08:03 AM, Tristan Croll wrote:

...

If you're installing a locally downloaded package with apt-get, you need to provide the path to the file (even if it's in your current working directory), i.e.:

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

-- Tristan

*From:* ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Stephen P. Molnar via ChimeraX-users chimerax-users@cgl.ucsf.edu *Sent:* 09 October 2021 12:50 *To:* goddard goddard@sonic.net; ChimeraX Users Help chimerax-users@cgl.ucsf.edu *Subject:* Re: [chimerax-users] ProblemI am attempting he installation of ChmimeraX Installing ChimeraX on Debian mv-10 � An interesting suggestion, but

comp@AbNormal:~/Downloads/ChimeraX$ sudo apt-get install ucsf-chimerax_1.2.5-1_amd64.deb [sudo] password for comp: Reading package lists... Done Building dependency tree������ Reading state information... Done E: Unable to locate package ucsf-chimerax_1.2.5-1_amd64.deb E: Couldn't find any package by glob 'ucsf-chimerax_1.2.5-1_amd64.deb' E: Couldn't find any package by regex 'ucsf-chimerax_1.2.5-1_amd64.deb' comp@AbNormal:~/Downloads/ChimeraX$

None of the missing packages are available via Synaptic.

On 10/08/2021 04:10 PM, Tom Goddard wrote:

...

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

-- Stephen P. Molnar, Ph.D. www.molecular-modeling.net http://www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

-- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users