You are viewing a single comment's thread from:
RE: Pin1 - Using Cystallography & NMR structures in Pymol to unveil a proteins function & structure
Nice one @clausewitz
I have worked on this platform once in my masters, now I just to use it again for some short peptides. There is something you might help.
Instead of taking any PDB ID or a protein of higher size (around 5-20 KDa), I want to make it for a tri or pentapeptide with modifications at both the terminals.
Is it possible to make one?
And, these peptides will be further self-assemble to give mostly beta-sheets. So I want to make a demo using pymol.
Hey, yeah Pymol have a builder tool which is easy to use for peptides and modifications, but making something self assemble is another question :).
Just click builder, residuals and pick the amino acid you want, 1 by 1 and you have the designed peptide in pymol.
Here is the tritide DQV in pink, and sticks, The white ball thing tells you where next residual will sit.
It might be hard to do a self assembly, or I have never animated such interactions in anyway.
I just tried to import many peptides, that´s no problem but to make frames of value is hard, you could move them 1 by 1 and make frames, and beta sheet can be formed lastly.
But I think pymol is hard to use for this purpose!
I ll come back if i find something.
Thanks @clausewitz
Addiion of amino acid I can do but unable to add any other organic group to the the terminals. Is it possible?
If I am working with a pentapeptide and want to make a model of its secondary structure. A single molecule is not going to form the whole structure only after assembling themselve it will form structure. If I know the typeof interaction happening in it, can I make one from pymol also which dipicts the whole phenomenon.
Thanks
Hey! Just build the peptid, click 1 atom, then now use the alternative under build called framgnet, click what you like to add.
Here is two amino acids imported on each other, both with a bromine group, and lastly a cyclo pentante on the lower residual, closing both of the Amino acids in:) just for the fun look of it :)
Cyclopenate in Pink + Bromine in red.
It worked..... thanks
I'll see for the assembling part
Thanks once again
Anytime :)
Yeah that part is harder, and after talking to some colleges we would recommend a graphical designer, not engineers in biochemistry hehe
Best of luck!