VMD-L Mailing List

From: Manish Agarwal (zmanish_at_gmail.com)
Date: Mon Jan 24 2011 - 17:48:07 CST

It is _indeed_ about visualization! To be able to make "pretty
pictures" and to "see" transitions in a trajectory, for example.

I already have parameters using which I can assign "helix/coil/turn"
to backbone atoms.
(My chain is a carbon backbone with hanging methyls and no hydrogens)

If I want to see everything as a "coil", then
is this the way to start?

set sel [atomselect top all]
$sel set structure coil

can this structure information be used to draw a "newcartoon" or a
"cartoon" for that matter?

In essence is it possible to derive structure information from
anywhere else except STRIDE?

Thanks,
Manish Agarwal
<zmanish_at_gmail.com>
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On Mon, Jan 24, 2011 at 5:42 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, 2011-01-24 at 16:43 -0500, Manish Agarwal wrote:
>> Dear VMD users,
>>
>> Is it possible to see the secondary structure of polymers like those
>> seen via the newcartoon in a typical protein? I would like to see the
>> helix formed in polypropylene for example, which  crystallizes into a
>> 3/1 helix. Is there something like STRIDE for polymers?
>
> no.
>
> if it is only about visualization, you can assign
> secondary structure codes to "backbone" atoms
> manually via Tcl scripting.
>
> axel.
>
>>
>> Thanks!
>> Manish Agarwal
>> <zmanish_at_gmail.com>
>> - - - - - - - - - - - - - - - - - - - - - - - - - - -
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>