VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 24 2011 - 21:27:07 CST

On Mon, Jan 24, 2011 at 6:48 PM, Manish Agarwal <zmanish_at_gmail.com> wrote:
> 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?

yes, also you have the following type codes:
alpha-helix: H
3-10 helix: G
pi-helix: I
beta-sheet: E
bridge: B
turn: T
coil: C (this is also the default)

> 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?

yes, but you also have to make VMD believe that you have a protein
backbone, i.e. you need the atom types C, N, CA and O for guidance
on orientation of the graphical elements.

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

yes, but it is up to you to provide the info.
check out the sscache script that avoids
having to call stride and caches the results
instead which speeds up display a lot.

cheers,
    axel.

> Thanks,
> Manish Agarwal
> <zmanish_at_gmail.com>
> - - - - - - - - - - - - - - - - - - - - - - - - - - -
>
>
>
>
> 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.
>>
>>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.