VMD-L Mailing List

From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Mon Aug 27 2018 - 04:41:46 CDT

Thanks a lot Jerome and Daniel

I would give them a try soon and see how they work out.

On Mon, Aug 27, 2018 at 2:31 AM, Daniel Möller <
daniel.moeller3_at_uni-greifswald.de> wrote:

> Hi,
>
>
>
> VMD normally just check the secondary structure once and will show this
> the whole frames. But there is scachebunch:
>
> https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscachebunch/
>
> which is an improved version of sscache:
>
> https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/
>
>
>
> They’re going through your loaded trajectory and will save every secondary
> structure per frame (calculated with stride).
>
>
>
> I don’t know if this are in the default installation, but you could load
> them from the links above. (stride should be default)
>
>
>
>
>
> Sincerely
>
>
>
> Daniel Möller
>
>
>
>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> *Im Auftrag von *Peter
> Mawanga
> *Gesendet:* Montag, 27. August 2018 09:41
> *An:* Vmd l <vmd-l_at_ks.uiuc.edu>
> *Betreff:* vmd-l: Secondary structure representation stays static
>
>
>
> Hello VMD users
>
>
>
> I have a cluster of small peptides bound to a membrane surface and I would
> like to visualise the secondary structure changes in them over the
> simulation period.
>
>
>
> I have run Timeline, and although I could see the secondary structure
> changes in the Timeline plot, but they are not reflected in the New Cartoon
> representation of the peptides over the simulation trajectory.
>
>
>
> Could someone please suggest a way to overcome this issue? I am using VMD
> 1.9.3.
>
>
>
> --
>
> Thanks
>
> Peter
> 

-- 
Cheers
Peter