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.
@MolecularMemory5 жыл бұрын
Awesome, thank you!!
@sabrango4 жыл бұрын
It did nothing to my command ! still says ACH syntax error
@fatihasulthana67314 жыл бұрын
It's nonsense
@virusworldjys4 жыл бұрын
"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 Жыл бұрын
@@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.
@kkssy1414 жыл бұрын
This is the BEST PyMOL tutorial. Thank you so much.
@MolecularMemory4 жыл бұрын
Oh hey! What a compliment. Made my day. Thank you!
@wurstuk5 жыл бұрын
Great Tutorial! in 23 minutes i learned more than i learned in my three dump uni exercises to this subject.
@TheMarcosVerissimo3 жыл бұрын
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.
@robertcormia79707 ай бұрын
The series with KP only gets better and better, this series is invaluable for students
@jakstat98805 жыл бұрын
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!!!
@MolecularMemory5 жыл бұрын
I'm delighted to hear this was helpful to you in your research! Thanks for watching.
@zosimospan89174 жыл бұрын
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!
@MolecularMemory4 жыл бұрын
Hey thank you for watching and leaving me a comment! I'm so glad to hear it was helpful.
@katzenpapa3 жыл бұрын
I am prepping for a master's exam - here is a GREAT BIG THANKS!!
@leowan33604 жыл бұрын
This is so helpful for students like me to get start. Thanks.
@duvvurum5 жыл бұрын
Many thanks, probably the best Pymol video.
@amazai10 ай бұрын
I really appreciate your energetic voice and teaching style😀
@onyemachukwuebukathankgod75965 жыл бұрын
I wish i could love this more than once. Really cleared my challenges. Thanks so much.
@MolecularMemory5 жыл бұрын
I am so glad! Thank you for watching!
@mrlifferth3 жыл бұрын
I really appreciate the addition of the colorblind-friendly color code!
@davidszone27883 жыл бұрын
Excellent tutorial. Very clearly presented. Keep up the great work! I will be pointing my students and postdocs to your highly informative videos.
@rayanimetime726 күн бұрын
I LOVE THIS VIDEO THANK YOU HELPED ME IN MY ASSIGNMENT
@mahshid80253 жыл бұрын
Pretty informative, thanks. I come back to watch it again once in a while.
@zecarim11 ай бұрын
thank you for this it literally saved my semester
@jeromeanthonyalvarez42414 жыл бұрын
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
@ArtemisXu-o5e11 ай бұрын
Wow great video! Well explained and detailed. Great enthusiasm
@milicaplavsic39 Жыл бұрын
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!
@Wherever_I_Go3 жыл бұрын
VERY WELL EXPLAINED.BEST VIDEO FOR BEGGINERS
@zhanghan46573 жыл бұрын
nice videos, I have learned a lot from it as the freshman. especially for the measurement of the hydrogen bond.
@twly4 жыл бұрын
This is EXTREMELY helpful!
@mahewashkhan2035 Жыл бұрын
Bestest video on pymol thank you so much! It helped me a lot :)
@mayarasantos5743 жыл бұрын
Hi, thanks for the video!!!!! I' m a doctor degree in Brazil. Thanks for your help
@SM-xn9bv4 жыл бұрын
I can not thank you enough! very helpful tutorial - very informative and concise!!! and those links are so useful! Many many thanks!
@vibhanshusingh3425 Жыл бұрын
Your videos are so amazing and easy to understand. please make more videos for other software like swiss model expasy. love from india.....
@MolecularMemory Жыл бұрын
This is a great idea! Maybe in the future I can tackle this. Thanks for watching!
@shubhammittal24215 жыл бұрын
Wow. Great video. Highly informative. Thanks!
@theanimalreporter95354 жыл бұрын
Sincere thanks for this amazing tutorial. Great Job!!
@saishradhareddykommidi45463 жыл бұрын
Thankyou for the video. It is very helpful.
@aliabghari97964 жыл бұрын
Very informative with practical examples!
@cesaralbertogonzalezguzman46422 жыл бұрын
Thank you so much! Definitely I subscribe to your channel. Pure high quality content.
@michaelmyerz52783 жыл бұрын
Thanks a lot. This was easy to follow and quick
@mariajosereysanchez55113 жыл бұрын
The video was incredible! Thanks so much for it!
@liecrower6133 Жыл бұрын
Thank you so much for this video and the commands! It´s amazing
@terriblast80764 жыл бұрын
Very nice tutorial. I really appreciate sharing some tip and tricks. Very helpful indeed.
@melekhajji84474 жыл бұрын
So helpful ! Thanks
@ancheung92523 жыл бұрын
it helps a lot, thank you!
@ashmitamainali10783 ай бұрын
Great tutorial..thank you!
@roselucca18074 жыл бұрын
Excellent tutorial! Thank you very much!
@hilalsukanar3315 Жыл бұрын
Wonderful tutorial, thanks!
@phasath3 жыл бұрын
Great video, thanks a lot.
@aboalifan1233 жыл бұрын
Thank you so much for this wonderful video, it really helped me so much, thumbs up
@MrFilu134 жыл бұрын
Thanks for the wonderful explanation
@gianfrancescogeraldinianto86843 жыл бұрын
Great video! Thank you so much for the help!
@FarhanHaqj3 жыл бұрын
Informative ! Good work
@saiprahalad153 Жыл бұрын
#lifesaver, thanks a lot. you made pymol fun!
@sderese5 жыл бұрын
A wonderful demonstrator
@InfiniteUniverse884 жыл бұрын
I haven't used the polar contacts feature before. Good to know.
@florianamaswa72582 жыл бұрын
Thank you this video you are genious
@evantang60865 жыл бұрын
It is a great job! Thank you very much.
@floo78005 жыл бұрын
Great Video. Greetings from Germany
@a222584614 жыл бұрын
Please make more Pymole video thank you so much helpful
@zimyang48523 жыл бұрын
Best video on this!
@zareaalzarea8362 жыл бұрын
thanks very very very much until the end of the world
@a222584615 жыл бұрын
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
@awadafuk48634 жыл бұрын
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
@a222584614 жыл бұрын
@@awadafuk4863 Pymole is not free and it charge money
@explore_with_pinku5 жыл бұрын
good demonstration. Thank you.
@muhammadyousuf28284 жыл бұрын
Nicely Explained...
@fouadel-shehabi99953 жыл бұрын
just perfect, thanks!
@akashpatel9023 жыл бұрын
Can you make the video for 2ANR protein
@NaveedHussainBiochemist3 жыл бұрын
Well explained!
@wizardlegend073 ай бұрын
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
@sagar17592 жыл бұрын
Really looking forward for protein-protein interaction appreciate🙏
@onatovonatovic5263 жыл бұрын
THANK YOU SO MUCH MUCH MUCH MUCK
@youngsha81745 жыл бұрын
Great!! It does help a lot!!
@MolecularMemory5 жыл бұрын
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! :)
@castilloh.gianmarco10482 жыл бұрын
Thanks video.
@robertcormia79707 ай бұрын
I wish she would show molecular docing of COVID (SARS) like HADOCK does
@shreyaverma1699 Жыл бұрын
Amazing
@andresordeixgrau41704 жыл бұрын
You are a Panther. Thanks!!
@fozshub49154 жыл бұрын
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
@suricate95414 жыл бұрын
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.
@philipconway12683 жыл бұрын
Thanks!!!
@hayneshera3 жыл бұрын
THANK YOUUUU
@zapy4224 жыл бұрын
Excellent
@fai80543 жыл бұрын
How to do “show non-bonded” for water molecules cause it doesn’t work with me
@jatinkashyap14914 жыл бұрын
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.
@rupachowdhury6164 Жыл бұрын
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??
@susmitmhatre45814 жыл бұрын
Great tutorial. I wanted to know if there is any way to predict the sitemap of the entire protein receptor using PyMOL.
@Anonymous-ni4tb3 жыл бұрын
Thank you so much!! By the way, is there a command to show nitrogen atom in blue and oxygen atom in red?
@DynastyyTV5 жыл бұрын
Thank you!
@ukaszgajda21383 жыл бұрын
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.
@yvonnesokoloveski72202 жыл бұрын
What if I do not have an molecule and really just my aa sequence? How do I find the active site?
@vitezjura4 жыл бұрын
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.
@kellaa41923 жыл бұрын
thank you for this! can you link your cheat sheet too?
@sarvarkakhkhorov99984 жыл бұрын
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?
@PokemonParadise20103 жыл бұрын
In PyMOL educational use, how do we do small molecule-protein interaction/docking?
@PokemonParadise20103 жыл бұрын
I do not have 'plugin' feature in my version of edu pymol..
@Appel.5 жыл бұрын
Thank you
@afssgq126 ай бұрын
Sorry, but how can i judged active site in sequence? why are you clicked "/B/A/998"?, is it catalytic(=active) site?
@manojkumarpatel21462 жыл бұрын
I want to join RNA nucleotides fro different strands. Can anyone suggest how to do it?
@ladieuquyen77074 жыл бұрын
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
@Hazi-to3ux4 ай бұрын
Ma'am how you add this cheat sheet into this vedio??
@cesargonzalez17764 жыл бұрын
Was that the interactions of the "oxyanion hole"?
@nadzamri56083 жыл бұрын
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.
@jaskaranwalia93444 жыл бұрын
hi how to mutant amino acid by formylglycine in pymol
@victuskordorwu8672 жыл бұрын
So what's the definite number of active sites?
@imrocknreeling3 жыл бұрын
How to find covalent interaction between receptor and ligand?
@arijitdas85582 жыл бұрын
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?
@DAR3_TO_WIN4 жыл бұрын
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?
@bonbonpony3 жыл бұрын
What are those dashed parts in the chain? (e.g at 1:18 in the top-right corner)
@AmanUllah-tk6wt2 жыл бұрын
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?