Pymol for beginners | Basic Tutorial Molecular Visualization of Proteins | Bioinformatics

This Tutorial will provide beginner guide to visualize protein molecule using Pymol
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[@bestofluck2225]

Waht a great video...sir please make video on docking and simulations .please it would be a great help.

[@jaannawaz2007]

Soon... Thank U

[@user-is2qq6gi7n]

@@jaannawaz2007 stfong

[@Anne-ry8hh]

Found the best video after searching for days. Absolute basics! Loved it! Thank you.

[@mogahidsabeel4988]

Thanks for the video! I wonder if you can help 🙏🏽, I am trying create crystallographic model BBI proteing from Vigna unguiculata (accession 2r33 in PDB) in order to visualize structural modifications caused by the aminoacidic differences between the analysed Vigna unguiculata accessions we are analysing. there 5 possible forms but we had proplems with 2 because their mutations are in the propeptide zone. my colleague said that there are few Vigna unguiculata BBIs in the database and in most cases they include a BBI + molecular target (like trypsin and chymotrypsin)

[@choukinou1616]

Very concise and informative. Excellent work. Thank you so much!

[@shreyosidey836]

Woww... Thank you so much sir.... This video is the best stepping stone for using pymol

[@anchma8837]

Thank you so much for this video! I was wondering is it possible to run animations on PyMOL, or should I integrate it with Blender or another 3D modeling program? I’d love to demonstrate some protein interactions for a club that I run at my Highschool!

[@hollypbird]

Thanks for making this video! Very helpful overview!

[@MrAdemyasin]

Hi Sir, thank you for the introduction. The undo and redo is not working. Is there any other option to return to the previous structure? It is very difficult to close the whole program and reopen it every time I do a mistake

[@meridawatson]

What to do if my target and Ligand are far apart when I open them in pymol? As in Ligand is not in active site of target, but separate

[@shalushama1459]

Sir could u pls tell me how we can presented our ball and stick structure or how we can analyze that their are ionic or covalent or which type of bonds are present

[@egs8545]

I have heard it is better to use APBS plug in rather than vacuum electrostatics can anyone tell me why?

[@hasriatunpadmi1640]

Please tell me the name of your protein in the video. I want to recreate that

[@monikumari5303]

How to see Cryo and x ray crystallography structure in pymol

[@Cooltija]

Thanks 👍

[@TheBioPedialalitdewalkar]

Thank you

[@sachusasvat4708]

If I have a protien drug complex for example "Human Transthyretin complex with diclofenac" how I am supposed to find protein part and drug part? Could you please help me out with it??

[@jaannawaz2007]

May in be next few weeks I am going to release advanced pymol session... U get above information in that video

[@labonihalder1003]

Thanks

[@hamoodelholandy]

Hi i want to ask how i can extract the proteins contact map for a given protein pdb file

[@jaannawaz2007]

you have to different toosl to get contact maps such as zhanglab.ccmb.med.umich.edu/NeBcon/

[@sonamgupta1062]

SIR is it mandatory to register ?

[@remyajames986]

Thank You Sir. It was very informative.

[@jaannawaz2007]

You are most welcome

[@rezakarimi6342]

great

[@rajniprasad9326]

How do I calculate docking score , docking energy n h-bonds

[@jaannawaz2007]

Check my videos in KZbin Channel page

[@premkumarkushwaha462]

How can we save high resolution images?

[@jaannawaz2007]

I already mentioned in the video.. if u have any errors u can post ur concerns in our Facebook page facebook.com/groups/261045198486665/

[@muhammadshahab1421]

Please make a vedio on publication images using ppt

[@jaannawaz2007]

You mean powerpoint?

[@walia5555]

Hi can you tell how to mutant amino acid by formylglycine and further it's conversation to gem-Diol.

[@walia5555]

And software used for it

[@jaannawaz2007]

Your question is not clear..

[@walia5555]

Sir i have doing molecular docking but problem in pdb file..

[@walia5555]

@@jaannawaz2007 in article the amino acid present and position 50 is mutant to formylglycine and then is convert to gem- diol

[@walia5555]

I do not no how it mutant to formylglycine and next step . I am simply mutant to glycine but not convert to formylglycine and next step..

[@sailenbarik8308]

Could you please eliminate that annoying background music next time. Otherwise nice video.

[@jaannawaz2007]

Sorry, for inconvenience... Yes, we removed background music for all other videos ...

[@tania3899]

I don't undenstand it's free or not?

[@jaannawaz2007]

Free Academic for limited time

[@nidhijindal22]

There's no need of a background music in the video. Its just an unnecessary strain to ears and mind.

[@HarisAzakidis]

Bro the music on the background is super annoying!

[@systum_101FR]

are you baba bangali ka gyan?