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<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">https://pypi.org/simple</a>,
<a class="moz-txt-link-freetext" href="https://cxtoolshed.rbvi.ucsf.edu/pypi/">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">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>
<br>
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</blockquote>
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