PyMOL Tutorial: Modeling the SARS-CoV-2 RBD Interactions with ACE (COVID-19 Coronavirus Proteins)

Love these videos thank you! A small time saving tip, instead of manually selecting all molecules within a chain you can just use the command: select chain A Alternatively you can use the command: split_chains this will split the chains into different objects while retaining contact information :)

Still getting used to Pymol--really happy I can get a tutorial mixed in with my current events! Thanks so much for this!

Best channel by far for modeling videos!

thank you so much, I LOVED this!! I really needed help finding interacting residues and this helped me out so much!!

For selecting chains, you can change the select mode to chains in bottom right corner, then you can revert back to residues. Time saver for me.

Thank you very much. You made my day

Thanks for the amazing video. This was simply fascinating. Any chance of doing a video to compare and contrast the spike proteins of the different variants? It is my understanding that the lambda variant has demonstrated mutations on the spike protein itself. Would love to see that in PyMOL. In any event, thank you for all of your hard work.

A million thanks! you saved me, you don't know how ahahaha A few days ago I started my research unit as a biochemist, but I had to work with bioinformatics, something that is seen very little or almost nothing in my career. My professor asked me to model the interaction of the Spike complex with ACE2, and I had only used PyMOL twice in my life to observe monomers.

Love your video so much. Thank you.

select interactionsiteAB, byres (chain B within 7 of chain A) or (chain A within 7 of chain B)

Thank you for your video. Well done.

Thankyou Molecular Memory for your wonderful educational videos and encouraging words. This will help us in our understanding of disease and structure, so we can become part of the cure in future. Right now, regarding your video on " Sars - Cov - 2 Structure ( Covid - 19 Coronavirus ) I wish to enquire about the Hydrogen Bonding between the Receptor Binding Domain ( RBD ) on the virus and the host Angiotensin Converting Enzyme 2 ( ACE 2 ) receptor. Is there any way that this bonding can be disrupted? I was considering Hydrogen Fluoride ( HF ) through appropriate water Fluoridation

Awesome. Thanks a lot!

Excellent video

To get contacts between chains (maybe?) you can do: action->find->polar contacts->between chains (bottom selection). I haven't tried this...

Hi, can you give us a tutorial on how to compare Docked Structure with PDB structure for the same RNA-protein complex? Thank you.

I wish this had more than just 2k views!

Very nice tutorial

Nice video, thanks so much! At ~10min, why not just show lines of interface area instead of the whole chain?

Thank you so much, it very helpful, but I still confused how to find non-polar contact in pymol? I do find- any contacts-between chains within5A ,then there get much dash lines within the same residues some are not OH or NH only C atom of Phenyl ? what does this mean? and then how to find that pi-pi interaction or other van der vals interaction?