Molecular Modeling

This video shows you how to visualize a file from the Protein Data Bank (www.pdb.org) using the software VMD from the University of Illinois (www.ks.uiuc.edu/).
This is a set of videos to help use VMD and NAMD for science class or lab projects. The videos step you through visualizing and simulating a protein to better understand how structure and function relate. For more information please see our article
"Molecular mechanics and dynamics characterization of an in silico mutated protein: A stand-alone lab module or support activity for in vivo and in vitro analyses of targeted proteins," Harry Chiang, Lucy C. Robinson, Cynthia J. Brame, and Troy C. Messina, Biochemistry and Molecular Biology Education, 9 Nov 2013.
onlinelibrary.w...

[@Royxu]

Well explained! Thank you!

[@TroyMessina]

No problem. Thank you!

[@sinhasuman1944]

Hi, great tutorial, thanks for that.
Please let us know if it's possible to colour only the the carbon atoms differently in vmd when two drug molecules are present in the structure..the non carbon atoms can have similar colour patters, eg red for oxygen and blue for nitrogen etc. as done conventionally.
Similarly, is it possible custom colour different parts (by parts i mean according to residue sequence eg. aa233 to 244 in red and 255 to 266 in white) of the same alpha-helix differently?
Sorry for the lengthy questions, hope you don't mind. Thanks for your patience.

[@TroyMessina]

Yes, all of that is possible. You can select single atoms, groups of atoms, single amino acids, groups of amino acids, or just about anything you want. That would be a long tutorial. I recommend you read VMD's user guide (www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node52.html) or search their email support (www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/).

[@MothaFawkenTeamGS]

is it possible to mutate a residue using this program?

[@TroyMessina]

Yes. th-cam.com/video/JiBKAZscPUo/w-d-xo.html. If you want to go in order of processing your files, here is a playlist. th-cam.com/play/PLNDQZCI_j92SQ_ipS8ZNxXswFeOsREX4e.html

[@SUNILKUMAR14]

nice..................

[@TroyMessina]

I appreciate it!

[@hesamodinmohammadian7564]

Hi
TNX

[@TroyMessina]

Thanks for watching!