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 :)
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.
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.
Oh WOW! That is convenient! Thank you so much! I still have to select the ligands separately, but it saves me fumbling around trying to select the chain within the sequence. Thanks so much for watching and leaving me a comment :)
@@MolecularMemory You can also type "sele chain A", this will select the chain AND the ligands - or directly rename and save the selection with "sele ACE1,chain A"
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?
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
I've been having issues, when selecting the end protein sequences, as it does not have /DA/B/712 but shows NAG NAG BMA in pink, which doesn't link to any of the other structures colours on my Pymol. any help would be great!
I got this from ur previous video but it did fade me here when we were manually selecting interchain residues that were interacting command: select NAME_SELECTION, byres SELECTION_NAME1 within 5 of SELECTION_NAME2
Isn’t easier if you just put: “show sticks, byres all within 5 of RBD” and then for ACE2? Then you can click on polar contacts -> to other atoms in object. I did it for each one and I obteined good distances. If you think i did something Wrong please write me.
I love the byres command and talk about it in another video! This looks like it should work. I'm having trouble executing it, though. For some reason, the byres command is showing the sticks for the whole protein, and not just at the interface in my model. I'll play around with this some more, and let me know if you did anything special that might help me out :) Thanks!
Molecular Memory YES! I saw your video so I thought about apply the idea and yes right, this command shows all the sticks for example for RBD1 y put it in the command but also you can get another sticks from the other molecule that you can select and do the same for the other molecule. You can save yourself a lot of work. Sorry maybe my english is not perfect but i hope these tricks work for you. Greetings from colombia!
@@valentinamonsalve4289 I was able to get this to work using the GUI buttons on the right! For the RBD object, I copied it. Then, I clicked A (action button) --> modify --> around --> residues within 5 A. Thank you for an excellent suggestion. Creo que su ingles es muy facil entender! Gracias por mirar mis videos, y muchas gracias por ayudarme! Voy a dar un workshop sobre PyMOL en una semana y utilizaré este estructura. Voy a demonstrar con este truco :) Saludos!
This is an interesting question, and I wish I had a good answer for you. Some of the interactions in the individual proteins are broken to create new interactions at the interface. I imagine it depends on both the number and strength of the interactions-interactions with ionic residues will be stronger than hydrogen bonds between things like OH groups. Again, wish I could answer you better, and thanks for watching!
Thanks for leaving me a comment. It seems like this should work! When I apply it though, this only shows the contacts within each separate protein (like, within the alpha helix), and not across the interface. So odd!
@@MolecularMemory The RU-vid servers take their time to encode all the different resolutions and they begin with the lower ones. One way is to keep the video set to "not listed" until all resolutions are ready (might be an hour or so).
