VMD-L Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Sat Nov 05 2011 - 00:38:29 CDT

Thanks a lot for the tip. But what about if you are making a movie?

On Nov 4, 2011, at 8:37 PM, harish vashisth <harish.vashisth_at_gmail.com> wrote:

> Hi,
> in order to re-render secondary structure for any frame along the trajectory...take the trajectory to that frame and in the tcl/tk console of vmd type the following command:
>
> vmd_calculate_structure <molid>
>
> if there is only one trajectory or molecule loaded, you can say: "vmd_calculate_structure 0" which will re-render the secondary structure for that frame..others may have better ideas on this mailing list, but this is what I do if i need to take a snapshot with secondary structure regenerated...
>
>
> On Fri, Nov 4, 2011 at 5:03 PM, Rabab Toubar <rtoubar_at_yahoo.com> wrote:
> I loaded my molecule in VMD, but the secondary structure representation didn't distinguish between the helix and the turns/coils. During generating the timeline for the same trajectory, I could see the correct structure representations in VMD. How could I fix that? I need to get the correct secondary structure elements to generate some figures and movies.
>
> Any input is highly appreciated
>
> Rabab Toubar
>