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.
assigns incorrect secondary structure. In my case, dss models a
complete transmembrane helix as a coil. Trying a manual repair in the
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?
From: Thomas Holder <speleo3@us...> - 2011-06-28 16:53:59
Matthias Schmidt wrote, On 06/28/11 13:37:
> 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
PyMOL calculates the consensus secondary structure over all states. You
may produce distorted intermediates with g_morph, so that consensus
might not be appropriate. To only consider first and last state, do this:
dss movie, state=-4
MPI for Developmental Biology