[chimerax-users] Error on installing isolde
Greg Couch
gregc at cgl.ucsf.edu
Mon Sep 27 15:24:31 PDT 2021
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.
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:
import chimerax
chimerax.app_dirs.user_data_dir
That will show where to go. For example, for me on Windows, it prints:
'C:\\Users\\gregc\\AppData\\Local\\UCSF\\ChimeraX\\1.2'
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, \.
The next step is to remove two directories: (1)
site-packages\ChimeraX_UI-1.2.1.dist-info, and (2)
site-packages\chimerax\ui.
And then, when you restart ChimeraX, you'll be back to the version that
came with ChimeraX.
HTH,
Greg
On 9/27/2021 2:22 PM, Greg Couch via ChimeraX-users wrote:
>
> Hi Haijing,
>
> 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.
>
> 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:
>
> toolshed uninstall ui
>
> 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.
>
> Best regards,
>
> Greg
>
> On 9/26/2021 5:55 PM, benhaijing--- via ChimeraX-users wrote:
>> Hi all！
>>
>> I can’t install the plugin isolde using command 'toolshed install
>> isolde'.
>>
>> Looking in indexes: https://pypi.org/simple,
>> https://cxtoolshed.rbvi.ucsf.edu/pypi/ 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.
>>
>> 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
>>
>> 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
>> https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
>> 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.
>>
>> Thanks,
>> Haijing Ben
>>
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>
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