Page Comparison

General updates

• JW – I sent out invites via Google Calendar. Realized this may have been the problem last time so I’ll probably send out some other sort of invite as well tomorrow.

  • Materials ready to go up?

  • JM – Very nearly ready to go.

  • JW – In the email, I’ll say that the materials will go up shortly.

• JW – On clockify, double check categories - You marked our check ins as OpenFE instead of OpenFF. I need you to resubmit Jan 1-7 timesheet since I had to withdraw it due to this error (I fixed it on the others).

  • JM – I can do that.

Workshop prep

Follow ups from last time

• JW – Remember that it’ll be very valuable in this talk to say what WON’T work as input. Can be formats, macromolecule types, or anything

• Look into whether pdbqr to pdbqt is safe to do with MDA

  • JM – Uses openbabel to generate atom types

Rehearsal notes:

• Install instructions?

  • Say “This will be best if you run it locally, I’ll show you two ways to run this with me. “

    • Download the workshop files and unzip them…

    • show how to install it locally using mamba, and mention that will go fast for you but not for other people.

    • Show how to to run on colab. Show what that looks like when it starts running, and then just say it will take a while to run, and colab might report that it’s crashed, but that’s all normal, and close the tab and proceed locally

• Explain whether we could have used the original ligand coords or if we needed to dock

• Your mouse is very small on the zoom window - Dwell longer and circle slowly on things you’re highlighting

• When referencing text using your mouse pointer, please highlight it since otherwise it’s hard to spot.

• See about getting a bigger mouse pointer

• JW will slack JM if he needs to square protein visualizations up

• For docking section, mention “autodock vina” early on, and then you can talk about DockString, but it might confuse people to talk about its SMILES-to-docking funcitonality, since we don’t use it.

• Mention that, for non-neutral ligands, the docking and solvating workflow won’t result in a neutral charge, so warn the audience and/or handwave about solutions.

• Have a backup for if the interchange creation takes 10 minutes again (maybe a pre-charged ligand and a code block to load it)