PyMOL: Working with Scenes (will save your butt!)

Building on my previous PyMOL tutorial with multiple ligands, improved commands, scenes, and basic measurement.

[@gustavogimenis]

Jesus your videos are so nice. I spent hours and hour of my life learning these tricks all by myself... Thank you!

[@nasserfaghih5345]

wow, that was the best video by far I've ever watched for PyMOL. thank you so much KP for sharing your experience with us.

[@ali_shoma2745]

You saved my life by "select active, byres all within 10 of ...." command. (Thank you)^infinity

[@amirmanzour3351]

I just started working with PyMol few days ago and I already feel like I'm comfortable with it. Just so amazing! Goal oriented, concise ,and pleasant to listen to and follow. I wonder if there is anything on working with RNAs as well. Also, would you have a recommendation for videos on basic chemistry on molecular bonds?

[@aboalifan123]

Thank you so much for this amazing video tutorial. You're the best. thumbs up

[@mdla1119]

This is really clear and helpful, thank you!!

[@marcosibarraguzman8453]

Excelente explicación muchas gracias ¡¡¡

[@user-hn9vu1zj9m]

Thank you so mush for these videos! And do you work with molecular dynamics, by any chance? :) I study PyMOL to analyse the results of MD simulations and your tutorials are very good and helpful.

[@ogunoluwamayowa4749]

Lovely tutorial, you just made protein modelling look like Kid's play..Please, can you demonstrate how a mutation(especially point mutation) will affect the active site and possibly the structure of the protein as regards the stability, folding etc? Thanks

[@MolecularMemory]

PyMOL does have a mutation wizard, but it doesn't change the active site-it only shows steric clash from nearby amino acids. Since I'm only able to show static images, maybe I can compare two crystal structures for you, one with an active site mutation. That would be a cool tutorial! Thanks for the comment and for watching.

[@ogunoluwamayowa4749]

@@MolecularMemory Thanks,that will be great

[@marvellous.concepts]

Thank u so much mam it helped alot🤝🤝

[@tusharkush7]

Your voice is so good!!

[@imrocknreeling]

Thank you ma'am

[@johirislam8174]

i want to visualize a protein protein complex docked pdb file by zooming the specific binding sites for publication.I already did the binding in pymol.But when i try to zoom the binding sites into word the figure is not very clear to see.So kindly help me on this.Thanks

[@lanthea3708]

Thank you for this nice tutorial! I have a question about the sphere size, as we know Mg(2+) has a radius about 80 pm and O(2-) about 140 pm (which I think water will have similar electron cloud size), is it a general rule (like, in publication) we still present the metal ion larger than the water oxygen?

[@MolecularMemory]

Often you will see metal ions represented a bit larger. I am not sure if there's rule for the ratio, but for me, it helps visually to see a bigger atom as bigger, even if we're knocking down the van der Waals ratio some. Thanks for watching!

[@ahmadibrahim7476]

instablaster

[@gaazijavaid]

How to draw dashed lines manually or via command between two atoms in a ligand to show any interaction. Please answer.

[@syarifuddinhusain6214]

You are so cool

[@dariomics8520]

According to observations from PDB it states the the angstrom range for H-bonds is 2.6-3.1 should we adjust our range accordingly?

[@MolecularMemory]

Such a great question. So the H bond length I typically see referenced is 1.5-2.5 Å. But, this is just for the H bond and doesn't take into account what we're actually measuring here, which is the distance between two oxygen atoms or an oxygen and a nitrogen (since the hydrogen atoms cannot be seen). So we have to add about an angstrom to account for the covalent bond. This gets me to a max of 3.5 Å measuring heteroatom to heteroatom. (Of course, the bond isn't linear, so that's a little complicated too). I think the max default for PyMOL to find polar contacts is 3.4 Å. So, 3.4 would be a weaker H bond, but that's where I kind of cut it off. If anyone has other insights, let us know!

[@dariomics8520]

Molecular Memory thank you for your detailed answer and very informative videos! They made pymol very easy to understand and will be a huge help in biochem

[@meijieliu8160]

hi ,could i ask why on my side there is no magnesium showing

[@SamDig]

OMG, seated, and eating a sandwich..... :O :)

[@prathvisingh8288]

Nice tutorial but how to compile the scenes together to make a movie?

[@MolecularMemory]

kzbin.info/www/bejne/pGOrloyFpbWUbq8 :D Thanks for watching!