PyMOL_Mover for PyRosetta installed via anaconda

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    • May 24, 2019 at 10:06 pm #3157
      Anonymous

        I have successfully installed PyRosetta via anaconda by command of “conda install pyrosetta” in Linux (Windows subsystem Linux) according to this instruction.

        http://www.pyrosetta.org/dow

        I have also confirmed several PyRosetta command indeed works well, so tried to utilize PyMol Mover. However, I failed to find “PyMOLPyRosettaServer.py” in Pyrosetta folder in anaconda package or elsewhere. The server file should be required for PyMol Mover. How can I connect Pyrosetta with PyMol? Or, conda-based installation did not still adopt PyMol Mover? Or, is there other way to connect Pymol and Pyrosetta than using “PyMOLPyRosettaServer.py”?

        If you need further info, please let me know. Thanks in advance for your kind help.

      • May 24, 2019 at 10:57 pm #14744
        Anonymous

          This is on my list. In future conda builds we will include these scripts. For now you can do the following: from http://www.pyrosetta.org/dow download one of the archive packages and from archive extract PyMOLRosettaServer.py or PyMOLPyRosettaServer.python3.py scripts. Hope this helps,

          • May 25, 2019 at 12:20 am #14745
            Anonymous

              Thanks for your suggestion!

              I extracted PyrosettaServer.py file, and placed it in the following folder

              C:Userskt<<Username>>AppDataLocalPackagesCanonicalGroupLimited.UbuntuonWindows_79rhkp1fndgscLocalStaterootfshomekt<<Username>>.pyenvversionsanaconda3-5.3.0pkgspyrosetta-2019.19+release.5adc612f-py36_0libpython3.6site-packagespyrosetta

              Then, I executed the py file from Pymol installed in windows. however, some errors ocurred.

              File “C:UsersktAnaconda3libsite-packagespymolinternal.py”, line 323, in file_read

                  handle = open(finfo, ‘rb’)

              FileNotFoundError: [Errno 2] No such file or directory: ‘PyMOL-RosettaServer.python3.py’

              During handling of the above exception, another exception occurred:

              Traceback (most recent call last):

                File “C:UsersktAnaconda3libsite-packagespymolinternal.py”, line 327, in file_read

                  raise pymol.CmdException(‘failed to open file “%s”‘ % finfo)

              pymol.CmdException:  Error: failed to open file “PyMOL-RosettaServer.python3.py”

              This may be because I placed the PyrosettaServer.py file in the wrong place, or I should execute the py file through Pymol installed on Linux. How can I deal with this problem? 

            • June 24, 2019 at 6:56 pm #14789
              Anonymous

                The issue you’re running into is that PyMol is assuming the script will be found in your executable path, rather than as part of the PyRosetta package.

                You probably want to manually install things to C:Userskt<<Username>>AppDataLocalPackagesCanonicalGroupLimited.UbuntuonWindows_79rhkp1fndgscLocalStaterootfshomekt<<Username>>.pyenvversionsanaconda3-5.3.0bin (to install things in your default conda environment) or into C:Userskt<<Username>>AppDataLocalPackagesCanonicalGroupLimited.UbuntuonWindows_79rhkp1fndgscLocalStaterootfshomekt<<Username>>.pyenvversionsanaconda3-5.3.0envs<<environment_name>>bin (to install it for a particular conda environment.

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