From: Neelanjana Sengupta (
Date: Sun Jun 07 2015 - 15:48:40 CDT

Hi Thomas,

Thanks for the pointer; it is indeed useful. However, what I need is a bit
more complicated...

Suppose I have a known structure, say "A-coil1-B-coil2-C", obtained from
the PDB database, where 'A', 'B', and 'C' are secondary structural
elements, connected by coil1 and coil2. I would like to modify coil1 and
coil2 (by changing both their sequence and length), but retain the original
relative orientations and hydrogen-bonding of A, B and C.

VMD community: any suggestions about this?


On Wed, Jun 3, 2015 at 7:55 PM, Thomas C. Bishop <> wrote:

> 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
> 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