I installed open-source pymol software using miniconda4 which have been installed successfully. I worked with the software, but whenever I am shutting down my PC and again restarted, the >pymol command on miniconda4 to open Pymol is not working. It is neither showing error nor opening. When I am trying to reinstall it, it is showing pymol is installed in my computer, and suggesting to reinstalled. It happened more than once. Now I am in a situation, whenever I am needing this software, I am installing it afresh or cannot shut down my PC. Can anyone shed some light on this problem and how to work on it?

  • 1
    $\begingroup$ The installation via conda only is one of the options. Did you try the installation via the package manager of your distribution (example Debian's tracker), or the images published here? In case you use Windows as OS, hovering over the .zip archive reads «unzip and run PyMOLWin.exe -- that simple!» like about a portable executable that will not nest into the PATH variable; would this be an option for you? $\endgroup$
    – Buttonwood
    Commented Dec 22, 2021 at 12:03
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    $\begingroup$ Do you use environments with conda? The executable will be accessible only in the environment where there were installed. Also, try to manually add the installation folder to the system path. $\endgroup$
    – Camps
    Commented Dec 22, 2021 at 12:42
  • $\begingroup$ To illustrate @Camps' comment about environments, compare the pattern used e.g., for the installation and use of RDKit with conda (outlined, e.g., in RDKit's documentation). $\endgroup$
    – Buttonwood
    Commented Dec 22, 2021 at 13:35
  • $\begingroup$ It might be helpful to include the details like OS and with what shell you are typing the pymol command in. If you are using linux, which pymol should give you the path where pymol is installed and in normal circumstances if it can't find it, there should be an error. $\endgroup$ Commented Dec 23, 2021 at 11:37
  • $\begingroup$ This question has been closed as it seems to be abandoned. It can be reopened if someone wants to add an answer or the OP addresses questions/suggestions in the comments. $\endgroup$
    – Tyberius
    Commented Jan 18, 2022 at 15:30


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