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?
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.
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
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.
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?
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!
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
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!
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
![Lp. Последняя Реальность #97 ЧЁРНАЯ МАТЕРИЯ [Анти Скинт] • Майнкрафт](http://i.ytimg.com/vi/k4MjXCzKsYw/mqdefault.jpg)
Jesus your videos are so nice. I spent hours and hour of my life learning these tricks all by myself... Thank you!
This is really clear and helpful, thank you!!
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.
Thank you so much for this amazing video tutorial. You're the best. thumbs up
You saved my life by "select active, byres all within 10 of ...." command.
(Thank you)^infinity
Excelente explicación muchas gracias ¡¡¡
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?
Thank u so much mam it helped alot🤝🤝
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.
Thank you ma'am
Your voice is so good!!
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
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.
@@MolecularMemory Thanks,that will be great
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?
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!
instablaster
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
You are so cool
How to draw dashed lines manually or via command between two atoms in a ligand to show any interaction. Please answer.
hi ,could i ask why on my side there is no magnesium showing
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?
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!
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
Nice tutorial but how to compile the scenes together to make a movie?
ua-cam.com/video/n2HeYOpPa8M/v-deo.html :D
Thanks for watching!
OMG, seated, and eating a sandwich..... :O :)