Visualizing bio-molecules in Computer[Part-1]: Let us inspect a PDB file and see it using VMD
View this post on Hive: Visualizing bio-molecules in Computer[Part-1]: Let us inspect a PDB file and see it using VMD
View this post on Hive: Visualizing bio-molecules in Computer[Part-1]: Let us inspect a PDB file and see it using VMD
FLIPPEN AMAZING. Its incredible what computers c\an do and how they are helping us move forward in the world. My friends studying chemistry had no clue what this software was but were as amazed as i am by this post. Thank you for sharing!!
Glad to hear that you liked it.
Nice work @dexterdev!
I made my Master final thesis in structural bioinformatics. PDB format is so ugly... I had to deal with it, topologies, and force fields files, it was a bit exasperating!
Cheers!
why PDB format is ugly?
I don't like the fact that it is a fixed-width column format. When I worked with PDB files, I used to make changes in the PDB files (because of project needs) and these changes, habitually used to generate errors in the file :S
It seems a little archaic format to me.
hmm :)
Nice one @dexterdev Its somewhat similar to the struture visualization in pymol, never tried VMD though. Going to definitely try it, thanks for sharing.
Pymol is user friendly I think. But vmd is more powerful as I understand.
I sometimes wish I could really communicate and understand the codes defined in the system more about bio-molecules but i like the way you simplified the interpretation for better understanding...Good work sir Dav
There is no complicated code here. All what I have explained is the format of a pdb file which is fairly simple. Let me know if you have any doubt.
No doubt...am just admiring the placement of codes while describing molecules..
No doubt...am just admiring the placement of codes while describing molecules..
Awesome work @dexterdev, thank you for providing a download source for the VMD software and valuable info regarding the content and format of PDB files.
Biomolecular engineering (is that right?) is not my field, however I do realize the significance of tutorials for young scientists.
Thank you for you efforts!
Thank you. Computational biophysics may be more apt to call this.
Thanks for the response.
Thanks @dexterdev. Am really swayed by this software. Can this version of PDB file be used in computational chemistry for molecule structure and properties? Thanks
PDB file format can technically encode any molecule. So it should be. (although PDB is protein data bank)
If you are asking about VMD software, if you have a valid PDB file you can use it. VMD also supports other formats.
Okay. Thanks. It's been awhile we chat!!!.