Hey thanks for the video. When I copy-pasted your command: show sticks, byres all within 5 of ACH I got invalid syntax error pointing at the s in sticks. Tried without s and it worked.

Great Tutorial! in 23 minutes i learned more than i learned in my three dump uni exercises to this subject.

Thanks for this video! I'm a physicist "gone rogue", starting research on molecular dynamics and docking. This has been so useful! Not only I learned more PyMol stuff, but I also learned some new (for me) biochem.

This is the BEST PyMOL tutorial. Thank you so much.

The series with KP only gets better and better, this series is invaluable for students

I'm currently solving my first structure of an enzyme and this has been such a massive help. My PI and I are immensely grateful for your video!!!

Wonderful tutorial. I am a graduate student studying structural biology. This was so well paced and clearly explained; helped me really get to grips with how to use Pymol to work smarter, not harder. Thank you so much!

I am prepping for a master's exam - here is a GREAT BIG THANKS!!

This is so helpful for students like me to get start. Thanks.

I really appreciate your energetic voice and teaching style😀

I really appreciate the addition of the colorblind-friendly color code!

I'm a current student and I am new to protein structures. This is when I hit SUBSCRIBE! Thanks for the best tutorial ever! :D

Excellent tutorial. Very clearly presented. Keep up the great work! I will be pointing my students and postdocs to your highly informative videos.

Many thanks, probably the best Pymol video.

I wish i could love this more than once. Really cleared my challenges. Thanks so much.

Pretty informative, thanks. I come back to watch it again once in a while.

thank you for this it literally saved my semester

Wow great video! Well explained and detailed. Great enthusiasm

Hi, thanks for the video!!!!! I' m a doctor degree in Brazil. Thanks for your help

This video was amazing! You are an great speaker and are able to explain things so well! Thanks for all the tips in this video!

VERY WELL EXPLAINED.BEST VIDEO FOR BEGGINERS

nice videos, I have learned a lot from it as the freshman. especially for the measurement of the hydrogen bond.

This is EXTREMELY helpful!

Bestest video on pymol thank you so much! It helped me a lot :)

I can not thank you enough! very helpful tutorial - very informative and concise!!! and those links are so useful! Many many thanks!

Your videos are so amazing and easy to understand. please make more videos for other software like swiss model expasy. love from india.....

Thank you so much! Definitely I subscribe to your channel. Pure high quality content.

Thankyou for the video. It is very helpful.

Wow. Great video. Highly informative. Thanks!

Sincere thanks for this amazing tutorial. Great Job!!

So helpful ! Thanks

Very informative with practical examples!

Thank you so much for this video and the commands! It´s amazing

I haven't used the polar contacts feature before. Good to know.

Thanks a lot. This was easy to follow and quick

thank you so much, this helps me a lot

The video was incredible! Thanks so much for it!

Very nice tutorial. I really appreciate sharing some tip and tricks. Very helpful indeed.

Thank you so much for this wonderful video, it really helped me so much, thumbs up

it helps a lot, thank you!

please can you do a tutorial on predict putative ligand binding sites based on physicochemical properties, conservation analysis, and structural constraints and also protein refinement and looping of modelled protein

Great video, thanks a lot.

A wonderful demonstrator

Great tutorial..thank you!

This is brilliant please make more enzym modelling video since I have no idea to identify the active side of each residue and draw it into ChemDraw

Wonderful tutorial, thanks!

Great video! Thank you so much for the help!

Best video on this!

Thanks for the wonderful explanation

thanks very very very much until the end of the world

Can you make the video for 2ANR protein

#lifesaver, thanks a lot. you made pymol fun!

Informative ! Good work

Great Video. Greetings from Germany

Please make more Pymole video thank you so much helpful

Really looking forward for protein-protein interaction appreciate🙏

It is a great job! Thank you very much.

Thanks for the video. Until now I couldn't manage to drag the molecule as I am using a laptop with a touch pad and couldn't find a solution if you could help. My laptop is Lenovo yoga 900

Thank you this video you are genious

Very helpful, thanks a lot!

Thanks for the tuitorial... I have a doubt like how can we edit rna.. Like I wanted to add methyl group to adenin base how did I do that??

How to do “show non-bonded” for water molecules cause it doesn’t work with me

Nicely Explained...

just perfect, thanks!

I wish she would show molecular docing of COVID (SARS) like HADOCK does

THANK YOU SO MUCH MUCH MUCH MUCK

I want to compare the binding site for estrogen of human estrogen receptor beta to potential binding site on the surface glycoprotein of CoV2. I have a theory estrogen might be binding to that protein because i found a small pocket of 19 aminoacids with 70 percent positives comparing the two proteins with BLAST as well as the near structure of 50 aminoacids next to this pocket has the same alpha helix structure predicted by HHpred. I am an amateur in using PyMOL however so I would appreciate if anyone else could compare this as well and use the results.

Well explained!

good demonstration. Thank you.

Hi Dr. KP, very informative playlist. I am looking to extract coordinates of active site residues with the Inhibitor. I am able to follow you until 9:05. And whatever I can see at 9:05 on the screen, I want to extract the coordinates of it in PDB format. To do it I guess I need to modify "show sticks, byres all within 5 of N3". So that the resulting structure will be saved as a selection. And then I can use the PyMol commands to extract the coordinates of that selection. Any hint, how I can do it. I am trying to study 6LU7.

Great video! I would be grateful if somebody could help mi with a basic issue. I obtained a full-length coding sequence of certain alpha-amylase. I determined the signal peptide for the CDS. In the next step, I would like to perform protein structure prediction with RaptorX. My question is: should I use a protein sequence without signal peptide, or should I use a full sequence (with a signal peptide) as an input? I fully understand that signal peptide is usually cleaved from the mature protein. However, I am not sure if the presence of the signal peptide sequence affects the prediction. I assumed yes, but I would like to consult this with more experienced users.

Amazing

You are a Panther. Thanks!!

What if I do not have an molecule and really just my aa sequence? How do I find the active site?

Thank you so much for this amazing video! It really helped me a lot for my manuscript. When I was watching the video, a question concerning hydrogen bonds came into my mind. In this introduction, you mention that hydrogen bond lengths are often in the range between 2.8 - 3.4 A. You also talk about the lengths of van-der-waal forces and ionic interactions. Do you have any citable reference for those values? I was looking for such a source, but I haven't found any suitable so far. Therefore, telling me the names of citable paper would be a great help and I would appreciate it very much! Thanks.

In PyMOL educational use, how do we do small molecule-protein interaction/docking?

hi how to mutant amino acid by formylglycine in pymol

I appreciate this video! But I am still unable to visualize the receptor-ligand (protein-protein) polar contacts after ClusPro and HDock docking by following the instructions. Is there any way to resolve this issue?

Sorry, but how can i judged active site in sequence? why are you clicked "/B/A/998"?, is it catalytic(=active) site?

Thanks video.

Thank you for your video but i have some problem with the motif and domain of protein, can you show me the way to see the motif or domain in reply here with one or to step by using the mouse. Thank you again

Hi Ma'am How to pinpoint an active site in the protein (target) when ligand is not attached to it. I mean not all structures in pdf have ligands given with it. How to go about in this case?

Thank you so much!! By the way, is there a command to show nitrogen atom in blue and oxygen atom in red?

Great!! It does help a lot!!

Excellent

I want to join RNA nucleotides fro different strands. Can anyone suggest how to do it?

Super helpful video, thank you so much! I downloaded a pdb file of a certain receptor-ligand complex from Protein Data Bank website, but when it came to finding polar contacts for the ligand to any atoms of the receptor residues which are 5 A away, it found no contact at all. Any idea why? Also, can I see pi-stacking in PyMOL?

THANK YOUUUU

Great tutorial. I wanted to know if there is any way to predict the sitemap of the entire protein receptor using PyMOL.

thanks. this was great!

Thanks!!!

Thank you for this wonderful tutorial. However, I'm not sure if you can help me as you're using a Mac and I'm on a Windows 10 PC, thus there may be different settings. Whenever I click on an residue individually like you do at 9:20, they just disappear instead of getting highlighted, so I've to redo the whole thing again. Am I doing something wrong?

can you please tell me how to delete a protein in a multi protein complex, how should this can be done?

Hey, at 18:04 , you mentioned that the range if suitable for vdw forces. May I know what range is okay for vdw forces? It would be helpful if you can help me finding the literature about a good range for vdw forces in protein-ligand interaction.

How to find covalent interaction between receptor and ligand?

Ma'am how you add this cheat sheet into this vedio??

Thank you!

What are those dashed parts in the chain? (e.g at 1:18 in the top-right corner)

thank you for this! can you link your cheat sheet too?

Thank you