[gmx-users] How to view evolution of secondary structure in a trajectory?

ms devicerandom at gmail.com
Thu Jun 17 02:44:54 CEST 2010

On 16/06/10 19:07, Chris Neale wrote:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/

Thanks a lot! I'll give it a spin ASAP.


> -- original message --
> Hi,
> I am trying -with no avail- to have a way to view a movie of a GROMACS
> trajectory with the secondary structure being updated automatically
> frame by frame (that is, changing colour and/or appearance accordingly
> during the trajectory).
> If I view the trajectory with VMD, even if I turn on "Update colour
> every frame", the secondary structure is always that of the frame where
> I turn its colour on first. With PyMol, it would require secondary
> structure within the PDB, but I've found no way to include, say, DSSP
> information within the PDB frames (I've googled and seen a few scripts
> linked, but links seem dead).
> Do you have any hint on where to look for this?
> thanks!
> m.

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