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I'm having an issue installing the open-source version of Pymol using Anaconda on Windows. I have Python 3.8.3 installed and when I try to add the package with Conda using conda install -c tpeulen pymol-open-source, I get the error

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - pymol-open-source -> python[version='>=3.7,<3.8.0a0']

Your python: python=3.8

Okay so it can't do Python 3.8? Not a problem, I'll just make a Python 3.7 virtual environment conda create -n "py37" python=3.7.9. Except, for some reason this still returns an error.

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - pymol-open-source -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0']

Your python: python=3.7

This claims that Python3.8 should work and the only version that doesn't work is 3.7! So, as a last attempt I tried switching to Python 3.6.12 and, sure enough, I got another error:

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - pymol-open-source -> python[version='>=3.7,<3.8.0a0']

Your python: python=3.6

This says only 3.7 will work, but that is clearly not the case. Am I using Conda wrong here or is there some issue with this package? How can I get the open-source PyMol installed properly?

Note: There is Incentive PyMol released by Schrodinger, which I could successfully install through Conda, but this is only a trial version. I would like to use the free version if possible.

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  • $\begingroup$ +1. I'm not sure which software tag is the most appropriate, but I've added software-assistance for now! $\endgroup$
    – Nike Dattani
    Oct 13, 2020 at 19:50
  • $\begingroup$ Ah, conda. A solution to a problem that was solved ~two decades ago by linux package managers, only with the joys of DLL dependency hell :D $\endgroup$
    – Susi Lehtola
    Oct 15, 2020 at 23:35
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    $\begingroup$ I'm seeing the same behavior with miniconda 4.9.2 running on the AWS Lambda Linux distribution with a variety of different python versions, all giving the same non-sensical version mismatch errors. Neither tpeulen/pymol-open-source nor awacha/pymol-open-source work, but schrodinger/pymol does. The open source versions install fine with the same version of miniconda on Mac OS X. Weird! $\endgroup$
    – Tom Morris
    Nov 17, 2020 at 20:00

2 Answers 2

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If you're using Linux its better if you install such packages using the apt-get method.

apt-get install pymol

I've encountered a similar error while installing MatPlotLib through conda.

For more info you can follow this link:

https://pymolwiki.org/index.php/Linux_Install

Hope this helps :)

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  • $\begingroup$ +1 I realized I left out that I'm on Windows, but I have WSL2 so this is also a helpful option. Answers for other operating are certainly welcome. $\endgroup$
    – Tyberius ♦
    Oct 13, 2020 at 22:08
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    $\begingroup$ +1. The original question didn't specify the operating system, so a Linux solution is a fair answer. If someone else gives an answer specific to Windows that would be even more helpful to the user, though I may point out that most users here probably use Linux (certainly there's been some trouble in getting help here for people using the Mac OS: mattermodeling.stackexchange.com/questions/tagged/…, one question is unanswered and one question has an answer only from the original person that asked the question). $\endgroup$
    – Nike Dattani
    Oct 13, 2020 at 22:16
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    $\begingroup$ +1, but Is there any source for better to use apt-get? I've been using Anaconda for a long time. I'd prefer to not have to use another way to install packages (e.g. there is already pip, conda, and now this) $\endgroup$
    – Cody Aldaz
    Oct 14, 2020 at 7:09
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I was able to find a workaround to get open source PyMol installed on Windows. Christoph Gohlke at the University of California has a large library of precompiled Python wheel files of various scientific packages, including PyMol. I was able to find a Windows version for Python 3.8 pymol‑2.5.0a0‑cp38‑cp38‑win_amd64.whl and after downloading this file, I was able to install PyMol using pip python -m pip install pymol‑2.5.0a0‑cp38‑cp38‑win_amd64.whl.

As mentioned on the PyMol wiki, I also had to pip install the pyqt5 package to get the graphical window working. I'm still puzzled why Conda didn't work, but at least it's possible to access this program on Windows.

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