For outreach, I made a spinning and blinking FITC-labelled Christmas tree (https://michelanglo.sgc.ox.ac.uk/r/christmas) using various Rosetta tools, which I have learnt to use properly thanks to all of you.
So using the excuse of the cheer of the holiday season, I wanted to sincerely thank all of you for all the help I have recieved in this forum! It has been invaluable and I really mean it.
Also, while I am at it, I must say a special thank you to Rocco Moretti, who seems to know the solution to any problem. Thank you!
Happy paper review season,
Wow I love this so much!! I'm keeping it for the rest of my life. :-D
Thank you Matteo for your most awesome gift, and I echo Matteo's gratitude to the Rosetta community for all of their incredibly generous help!
Happy holidays to all,
Aha, is this the final pdb? https://github.com/matteoferla/Christmas_tree_protein/blob/master/tree_final.pdb
Yes. It is.
Although I have been told that labelling a protein with more than one fluorescein is bad due to homo-FRET. Therefore, there ought to be a series of different dyes.
On a more serious note for any modders, the params file does not have conformers as I was not sure how to generate them for a covalently bound ligand, but I suspect that obabel --conformer with a mol2 with the connecting atom added (and last in index) and then removed from the outputs, would work. Due to the very drug like nature of fluorescein and implicit waters, ligand_dock does not work well for it anyway.