Superdev PyMOL plugin does not initialize

[Jarvellis Rogers]

Upon installing the FFEA plugin from the superdev version of FFEAplugin.tar.gz to PyMOL 1.8 the plugin cannot be initialized to be used, and the following error occurs:

FFEA_measurement will not load matplotlib, as it conflicts with PyMOL

No module named FFEA_rod

Unable to initialize plugin ‘FFEAplugin’ (pmg_tk.startup.FFEAplugin).

Error persists on PyMOL 2.3.5.

I’m aware of the common occurrence of this error noted in the docs for when PyMOL does not yet have a designated plugin folder but that isn’t what is causing this particular issue. Restarting PyMOL does not fix the error.

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Upon installing the FFEA plugin from the release build (2.6) onto PyMOL1.8, the plugin can be initialized but the following error persists:

FFEA_measurement will not load matplotlib, as it conflicts with PyMOL

This, however, does not stop the plugin from working. Therefore it seems that the FFEA_rod error is causing the initialization error and needs to be fixed.

[Robert Welch]

This is probably due to FFEA_rod not being correctly installed into /opt or into the viewer folder. I will have a look.

[Robert Welch]

These two will be fixed next time I push my commits to rod_dev.

[Ryan Cocking]

Installing the plugin from the master branch in PyMol 1.8.x does not initialise as of the (07-08-2020) release, as the indentation of __init.py__ is a mixture of tabs and spaces.

I fixed this on my end by converting everything to tabs in VSCode (in init.py > F1 > Convert indentation to spaces), but have yet to commit/push to any branch.

[Robert Welch]

Can you push a hotfix to superdev and then pull it to main? I can make sure the fix is included in the binary distribution.

[Ryan Cocking]

Yes, I’ll get on this. Just need to remember some git…

[Ryan Cocking]

With the changes Rob and I have made, I’m now able to get PyMol up and running from superdev with no issues. Can @Robert Welch and @Jarvellis Rogers please confirm?

[Jarvellis Rogers]

I tested this with my molecules and this seems to be working. I don’t have anything with rods to try to see if that still causes issues with the FFEA_rod module, but molecules that are generated from PDB files / EMD maps are working for me.

Edit: Tested with rods and that also works.

[Ryan Cocking]

Sorted this a while ago by forcing indentation of the PyMol plugin.