Sequence To Structure
1 answer
You can do it in pymol: http://www.pymolwiki.org/index.php/Peptide_Sequence
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This question does not make sense. Linear structure - what is that? - is by definition not 3D. PDB format by definition describes a 3-dimensional structure, not a "linear set of aminoacids." What, exactly, do you want to do?
I want the 3d arrangements of aminoacids, all with their constituent atoms, by linear i mean one after another where the c-alpha carbons fall on the same line, that is it could be just random i just want to be to be able generate them in the order they come in the sequence so that the software interprets them as contiguous.
Perhaps you could show an example. Still not making sense to me. What software requires this?
It's not about which software requires this, but this is what i want to do.
Guess I was fooled by the phrase "so that the software interprets them as contiguous" :) Anyway, how about that example?
I think the term he meant was 'extended' conformation. Use Pymol as described in Pappu's comment, easy enough!
I'm closing this question in the absence of any attempts to improve it.
As I said before, the "linear" sequence is still a valid term. He probably meant "extended", which is probably more correct, but linear is far from incorrect.. Besides, the question was answered quickly, the user just forgot to accept the answer..
User does not have a great recent record of accepting answers or responding to concerns. Happy to reopen - if they show interest.