[chimerax-users] Error on installing isolde

Mon Sep 27 14:22:53 PDT 2021

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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