Re: [chimerax-users] Error on installing isolde

7 Oct 2021


      Hi Greg!Thanks very much! After I deleted the two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info and (2) site-packages\chimerax\ui in my computer, I have successfully reinstalled chimerax and isolde! It works now!Best regards, Haijing Ben
----- 原始邮件 -----
发件人：Greg Couch <gregc@cgl.ucsf.edu>
收件人：benhaijing@sina.com, chimerax-users <chimerax-users@cgl.ucsf.edu>
主题：Re: [chimerax-users] Error on installing isolde
日期：2021年09月28日 06点24分

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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Re: [chimerax-users] Error on installing isolde

benhaijing＠sina.com