Hi

I am making a movie in pymol that I prepared with g_morph

g_morph -f1 start.pdb -f2 end.pdb -o movie.pdb -nofit (gromacs 4.5.4)

Pymol does not assign the secondary structure.

load movie.pdb
dss, movie

assigns incorrect secondary structure. In my case, dss models a
complete transmembrane helix as a coil. Trying a manual repair in the
form of

alter resi1-resi2/, ss='H'

does change the representation of the bespoke helix from a coil into a
helix cartoon. But in a few frames of movie.pdb, the representation is
changed to a "tube".

Why is that and how can I fix it?

Best,

Matthias

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