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<p>Actually, it worse than I thought. Uninstalling the
user-installed version of the UI bundle is not doable from within
ChimeraX. And uninstalling ChimeraX and reinstalling it doesn't
help, because that only takes care of system files, not any of the
user's customization.<br>
</p>
<p>To get rid of the user installed bundle, the first step is to
find where on the filesystem the files are. So start the Shell
tool from the Tools / General menu. And then type in it:</p>
import chimerax<br>
chimerax.app_dirs.user_data_dir
<p>That will show where to go. For example, for me on Windows, it
prints:</p>
<p> 'C:\\Users\\gregc\\AppData\\Local\\UCSF\\ChimeraX\\1.2'</p>
<p>So using the Windows file brower, I would navigate to
C:\Users\gregc\AppData\Local\UCSF\ChimeraX\1.2. You may need to
check "Hidden Items" in the View menu to navigate into AppData
directory. macOS and Linux users should have an easier time going
to the correct directory. And they would use forward slash, /,
instead of backslash, \.<br>
</p>
<p>The next step is to remove two directories: (1)
site-packages\ChimeraX_UI-1.2.1.dist-info, and (2)
site-packages\chimerax\ui.</p>
<p>And then, when you restart ChimeraX, you'll be back to the
version that came with ChimeraX.</p>
<p> HTH,<br>
</p>
<p> Greg<br>
</p>
<div class="moz-cite-prefix">On 9/27/2021 2:22 PM, Greg Couch via
ChimeraX-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:2c767c67-ef4e-b1fc-81b8-ae446ee9ca4f@cgl.ucsf.edu">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<p>Hi Haijing,</p>
<p>The output you pasted says that ISOLDE is already installed, so
you don't need to install it again. It should be reinstallable,
so that is a bug. If you use the graphical toolshed interface
(click on More Tools... in the Tools menu), you would have seen
that the install button for ISOLDE said Installed, meaning it is
already installed.<br>
</p>
<p>In this particular case, it looks you made things worse by
deliberately installing an older version of the UI bundle from
the toolshed than the version that came with ChimeraX. Using
the graphical toolshed interface, you would have seen that it
was a downgrade, which means do not install it unless
necessary. Or maybe you used the Updates tool to do that? If
so, you should have seen that installed version was 1.7.6 and
the version on the toolshed is 1.2.1, so much older. Regardless
of how you did it, to fix it, give the command:</p>
<p> toolshed uninstall ui</p>
<p>And that should revert back to version of the UI bundle that
came with ChimeraX. The fact that you could install an older,
incompatible, version of the UI bundle is a bug that is
difficult to fix in the general case.</p>
<p> Best regards,<br>
</p>
<p> Greg<br>
</p>
<div class="moz-cite-prefix">On 9/26/2021 5:55 PM, benhaijing---
via ChimeraX-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20210927005500.496104640472@webmail.sinamail.sina.com.cn">
<meta http-equiv="content-type" content="text/html;
charset=UTF-8">
<div>Hi all！</div>
<div><br>
</div>
<div>I can’t install the plugin isolde using command 'toolshed
install isolde'.</div>
<div><br>
</div>
<div>Looking in indexes: <a class="moz-txt-link-freetext"
href="https://pypi.org/simple" moz-do-not-send="true">https://pypi.org/simple</a>,
<a class="moz-txt-link-freetext"
href="https://cxtoolshed.rbvi.ucsf.edu/pypi/"
moz-do-not-send="true">https://cxtoolshed.rbvi.ucsf.edu/pypi/</a>
Requirement already satisfied: ChimeraX-ISOLDE==1.2.2 in
c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages
(1.2.2) Requirement already satisfied:
ChimeraX-AtomicLibrary~=3.1.0 in c:\program
files\chimerax\bin\lib\site-packages (from
ChimeraX-ISOLDE==1.2.2) (3.1.3) Requirement already satisfied:
ChimeraX-Core~=1.2.0 in c:\program
files\chimerax\bin\lib\site-packages (from
ChimeraX-ISOLDE==1.2.2) (1.2.5) Requirement already satisfied:
ChimeraX-Arrays~=1.0.0 in c:\program
files\chimerax\bin\lib\site-packages (from
ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied:
ChimeraX-Clipper~=0.16.0 in
c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages
(from ChimeraX-ISOLDE==1.2.2) (0.16.0) Requirement already
satisfied: ChimeraX-Atomic~=1.13.0 in c:\program
files\chimerax\bin\lib\site-packages (from
ChimeraX-ISOLDE==1.2.2) (1.13.2) Requirement already
satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from
ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0
in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from
ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1)
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0
in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
(1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0
in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
(1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0
in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
(1.5) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0
in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
(1.0.1) Requirement already satisfied:
ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from
ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
(1.4) Requirement already satisfied: ChimeraX-IO~=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
(1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0
in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
(1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in
c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages
(from
ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
(1.2.1) INFO: pip is looking at multiple versions of
chimerax-pdblibrary to determine which version is compatible
with other requirements. This could take a while. INFO: pip is
looking at multiple versions of chimerax-pdb to determine
which version is compatible with other requirements. This
could take a while. INFO: pip is looking at multiple versions
of chimerax-opencommand to determine which version is
compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of
chimerax-nucleotides to determine which version is compatible
with other requirements. This could take a while. INFO: pip is
looking at multiple versions of chimerax-io to determine which
version is compatible with other requirements. This could take
a while. INFO: pip is looking at multiple versions of
chimerax-dataformats to determine which version is compatible
with other requirements. This could take a while. INFO: pip is
looking at multiple versions of chimerax-mmcif to determine
which version is compatible with other requirements. This
could take a while. INFO: pip is looking at multiple versions
of chimerax-graphics to determine which version is compatible
with other requirements. This could take a while. INFO: pip is
looking at multiple versions of chimerax-geometry to determine
which version is compatible with other requirements. This
could take a while. INFO: pip is looking at multiple versions
of chimerax-core to determine which version is compatible with
other requirements. This could take a while. INFO: pip is
looking at multiple versions of chimerax-atomsearchlibrary to
determine which version is compatible with other requirements.
This could take a while. INFO: pip is looking at multiple
versions of chimerax-connectstructure to determine which
version is compatible with other requirements. This could take
a while. INFO: pip is looking at multiple versions of
chimerax-clipper to determine which version is compatible with
other requirements. This could take a while. INFO: pip is
looking at multiple versions of chimerax-atomiclibrary to
determine which version is compatible with other requirements.
This could take a while. INFO: pip is looking at multiple
versions of chimerax-atomic to determine which version is
compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-arrays
to determine which version is compatible with other
requirements. This could take a while. INFO: pip is looking at
multiple versions of chimerax-isolde to determine which
version is compatible with other requirements. This could take
a while. </div>
<div><br>
</div>
<div>The conflict is caused by: chimerax-nucleotides 2.0.1
depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends
on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on
ChimeraX-UI~=1.4 </div>
<div><br>
</div>
<div>To fix this you could try to: 1. loosen the range of
package versions you've specified 2. remove package versions
to allow pip attempt to solve the dependency conflict ERROR:
Cannot install chimerax-nucleotides==2.0.1,
chimerax-opencommand==1.5 and chimerax-savecommand==1.4
because these package versions have conflicting dependencies.
ERROR: ResolutionImpossible: for help visit
<a class="moz-txt-link-freetext"
href="https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies"
moz-do-not-send="true">https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies</a>
WARNING: You are using pip version 21.0.1; however, version
21.2.4 is available. You should consider upgrading via the
'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install
--upgrade pip' command.</div>
<div><br>
</div>
<div>
<pre style="white-space: pre-wrap;">Thanks,
Haijing Ben</pre>
</div>
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