Dear Users, Thank you very much for the suggestions! I was able to connect to a computer remotely to try them out. In case anyone else has issues with this in the future: homebrew does indeed work nicely with open source PyMOL and Rdkit. It turns out there was an issue with the Python pathways since Anaconda was already installed and therefore by default the Anaconda Python was being referenced. Once I made sure to specify the Python pathway that corresponded to homebrew, additional dependencies I needed (such as matplotlib) could be installed with pip.
Justine ________________________________ From: Thomas Holder <thomas.hol...@schrodinger.com> Sent: Wednesday, January 27, 2021 2:54 AM To: Justine Williams <justine.willi...@uwaterloo.ca> Cc: pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] Mac Installation Question Hi Justine, Have you tried with the official schrodinger::pymol package? If the user who wants to use your plugin has a PyMOL license, that should be the best option for him. conda create -n pymol -c conda-forge python=3.7 rdkit=2020.03.3.0 matplotlib seaborn pip numpy schrodinger::pymol schrodinger::tk scikit-learn git You can also test this without a license, PyMOL will run in evaluation mode but your plugin should be fully functional. Cheers, Thomas > On Jan 27, 2021, at 1:46 AM, Justine Williams <justine.willi...@uwaterloo.ca> > wrote: > > Dear users, > > Could someone please help me with installing open source pymol on MacOS? I > created a plugin, but to allow it to be more easily available to users with > different OS, I need to include installation instructions for installing open > source pymol on each. I prepared some installation instructions for creating > a conda environment that works with Windows and Linux, but am having some > issues getting the installation to work consistently for the MacOS case. As a > note, I am not a Mac user myself, and have been trying to troubleshoot > remotely with the help of colleagues who own Macs. > > I need to have the rdkit package usable to pymol, which is why I was creating > the conda environment. The general conda steps that worked for Windows/Linux > were to install and activate Anaconda3 > (https://docs.anaconda.com/anaconda/install/mac-os/). Next, to open a > terminal in the Anaconda3 directory named "envs." Then to use the following > command to create an environment named pymol with the packages necessary: > > conda create -n pymol python=3.7 rdkit=2020.03.3.0 matplotlib seaborn pip > numpy conda-forge::pmw tpeulen::pymol-open-source scikit-learn git > > Finally, to activate the environment: > > conda activate pymol > > The error that is generated for this approach is "ImportError: > dlopen(/Users/FarFar/anaconda3/envs/pymol/lib/python3.7/site-packages/pymol/_cmd.cpython-37m-darwin.so, > 2): Symbol not found: _glAccum" > > I would really appreciate any assistance with installation for Mac cases, or > if anyone knows of known issues with this. As of now, it seems like using > homebrew to install open source pymol and rdkit might be the best approach to > take, but I have not been able to get that working. If there are other > strategies for installing open source pymol and rdkit I would really > appreciate the help. > > Thank you, > > Justine > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
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