VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Wed Jun 03 2015 - 13:55:43 CDT

hate to draw folks away from VMD but swisspdb viewer does an excellent job at this sort of thing.
load a sequence and assign secondary structgure to whatever parts you like.

see
http://spdbv.vital-it.ch/

The question remains though can this be easily done in VMD?
what are other alternatives?

Tom


On 06/03/2015 10:14 AM, Neelanjana Sengupta wrote:
Dear VMD experts,

I have a peptide structure, which is "linker1-strand1-linker2-strand2-linker3" , where the strands are amino acid sequences of specific secondary structure (beta sheet actually), and the linkers are sequences that are coil-like.

I wish to create constructs like "linker1-strand1-linker2-strand2-linker2-strand3-linker3", etc. Is there a straightforward way to do this (versus the tedious way, where I chop everything, and get the end atoms close enough to form bonds)?

Thanks,
Neelanjana