VMD-L Mailing List

From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri Nov 04 2011 - 19:37:43 CDT

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
>