PyMOL: Active Sites in Minutes (Using only Sequence Info!)

How do you model an active site, when all you have is a PDB file? Dr. KP shows you time-saving techniques and commands for AS modeling in PyMOL.
Download PyMOL for free: pymol.org/edu/?q=educational/
Commands used in this video: docs.google.com/document/d/1y...
PDB ID: 2ace
Raves, M. L., Harel, M., Pang, Y. P., Silman, I., Kozikowski, A. P., & Sussman, J. L. (1997). Structure of acetylcholinesterase complexed with the nootropic alkaloid,(-)-huperzine A. Nature structural biology, 4(1), 57-63.

[@biofilms2435]

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.

[@MolecularMemory]

Awesome, thank you!!

[@sabrango]

It did nothing to my command ! still says ACH syntax error

[@fatihasulthana6731]

It's nonsense

[@virusworldjys]

"ACH" represents the "selection" that you would have named as shown at the beginning of the video. Note also that PyMOL is CasE SenSiTIve and that in the video the "h" was not capitalized, hence written as "ACh" - That in itself would create an error.

[@l3xxinthecity]

@@sabrango i think the code doesn't work for windows. EDIT: it also works for windows. Just check your code. Mine didn't work because of writing "showsticks" instead of "show sticks" go to the url she posted and just copy paste the code then put in the name if your selection.

[@TheMarcosVerissimo]

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.

[@wurstuk]

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

[@jakstat9880]

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!!!

[@MolecularMemory]

I'm delighted to hear this was helpful to you in your research! Thanks for watching.

[@kkssy141]

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

[@MolecularMemory]

Oh hey! What a compliment. Made my day. Thank you!

[@davidszone2788]

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

[@robertcormia7970]

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

[@duvvurum]

Many thanks, probably the best Pymol video.

[@milicaplavsic39]

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!

[@leowan3360]

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

[@onyemachukwuebukathankgod7596]

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

[@MolecularMemory]

I am so glad! Thank you for watching!

[@mahshid8025]

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

[@zosimospan8917]

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!

[@MolecularMemory]

Hey thank you for watching and leaving me a comment! I'm so glad to hear it was helpful.

[@SM-xn9bv]

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

[@mrlifferth]

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

[@jeromeanthonyalvarez4241]

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

[@katzenpapa]

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

[@amazai]

I really appreciate your energetic voice and teaching style😀

[@zhanghan4657]

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

[@theanimalreporter9535]

Sincere thanks for this amazing tutorial. Great Job!!

[@shubhammittal2421]

Wow. Great video. Highly informative. Thanks!

[@twly]

This is EXTREMELY helpful!

[@mariajosereysanchez5511]

The video was incredible! Thanks so much for it!

[@terriblast8076]

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

[@aliabghari9796]

Very informative with practical examples!

[@liecrower6133]

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

[@roselucca1807]

Excellent tutorial! Thank you very much!

[@user-fv8ey4zo6r]

Wow great video! Well explained and detailed. Great enthusiasm

[@michaelmyerz5278]

Thanks a lot. This was easy to follow and quick

[@zecarim]

thank you for this it literally saved my semester

[@evantang6086]

It is a great job! Thank you very much.

[@aboalifan123]

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

[@mahewashkhan2035]

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

[@explore_with_pinku]

good demonstration. Thank you.

[@gianfrancescogeraldinianto8684]

Great video! Thank you so much for the help!

[@cesaralbertogonzalezguzman4642]

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

[@Wherever_I_Go]

VERY WELL EXPLAINED.BEST VIDEO FOR BEGGINERS

[@FarhanHaqj]

Informative ! Good work

[@ancheung9252]

it helps a lot, thank you!

[@sderese]

A wonderful demonstrator

[@MrFilu13]

Thanks for the wonderful explanation

[@saishradhareddykommidi4546]

Thankyou for the video. It is very helpful.

[@justbae810]

thank you so much, this helps me a lot

[@melekhajji8447]

So helpful ! Thanks

[@jatinkashyap1491]

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.

[@floo7800]

Great Video. Greetings from Germany

[@sarvarkakhkhorov9998]

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?

[@catfish572]

thanks. this was great!

[@phasath]

Great video, thanks a lot.

[@nadzamri5608]

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.

[@NurulIslam-tl6ky]

Very helpful, thanks a lot!

[@ukaszgajda2138]

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.

[@ashmitamainali1078]

Great tutorial..thank you!

[@susmitmhatre4581]

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

[@DAR3_TO_WIN]

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?

[@fouadel-shehabi9995]

just perfect, thanks!

[@mayarasantos574]

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

[@InfiniteUniverse88]

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

[@muhammadyousuf2828]

Nicely Explained...

[@youngsha8174]

Great!! It does help a lot!!

[@MolecularMemory]

Awesome! At the beginning of the next PyMOL video (working with scenes) I figured out how to make the active site a selection with one typed command. Check it out! :)

[@zimyang4852]

Best video on this!

[@saiprahalad153]

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

[@NaveedHussainBiochemist]

Well explained!

[@suricate9541]

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.

[@rupachowdhury6164]

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??

[@a22258461]

Please make more Pymole video thank you so much helpful

[@florianamaswa7258]

Thank you this video you are genious

[@fozshub4915]

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

[@arijitdas8558]

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?

[@ladieuquyen7707]

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

[@bonbonpony]

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

[@a22258461]

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

[@awadafuk4863]

Hi Yen-Ting, I don’t know if you’ve come across this but the RSCB PDB has a 2-d view of ligand binding hidden on each PDB entry

[@a22258461]

@@awadafuk4863 Pymole is not free and it charge money

[@Anonymous-ni4tb]

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

[@DynastyyTV]

Thank you!

[@onatovonatovic526]

THANK YOU SO MUCH MUCH MUCH MUCK

[@vibhanshusingh3425]

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

[@MolecularMemory]

This is a great idea! Maybe in the future I can tackle this. Thanks for watching!

[@faizaarshad705]

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

[@AmanUllah-tk6wt]

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?

[@andresordeixgrau4170]

You are a Panther. Thanks!!

[@kellaa4192]

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

[@cesargonzalez1776]

Was that the interactions of the "oxyanion hole"?

[@mostafai.elandlos3353]

thanks for this video, i need your help when i show active site as sticks, it will be the same color of background and will not change never. what shall i do ?

[@MolecularMemory]

Once you have made a selection for the active site, you should be able to change the color from the menus (A, S, H, L, C) using the "C" command. Color by element to preserve the CPK coloring!

[@zapy422]

Excellent

[@jaskaranwalia9344]

hi how to mutant amino acid by formylglycine in pymol

[@fai8054]

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

[@Appel.]

Thank you

[@castilloh.gianmarco1048]

Thanks video.

[@hayneshera]

THANK YOUUUU

[@shakirullah5570]

How we can identify the active site of enzyme

[@vitezjura]

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.

[@akashpatel902]

Can you make the video for 2ANR protein

[@yvonnesokoloveski7220]

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

[@wizardlegend07]

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

[@imrocknreeling]

How to find covalent interaction between receptor and ligand?

[@noor-ul-ainmurtaza7117]

How to use rotate, translate and bond commands?

[@manojkumarpatel2146]

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

[@shreyaverma1699]

Amazing

[@sagar1759]

Really looking forward for protein-protein interaction appreciate🙏

[@philipconway1268]

Thanks!!!

[@PokemonParadise2010]

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

[@PokemonParadise2010]

I do not have 'plugin' feature in my version of edu pymol..