1CRN for example has disulphide bonds which are covalant and thats why set_dihedral does not work. I think its the bug, which tells you that it has been setted to zero. So you have to remove the disulphide bonds before setting the dihedral angles.

you can do so by

unbond r. cys and n. sg, r. cys and n. sg

and then

PyMOL>set_dihedral 21/n, 21/ca, 21/c, 22/n, 0.0
  SetDihedral: adjusted to 0.000

PyMOL>get_dihedral 21/n, 21/ca, 21/c, 22/n
  cmd.get_dihedral: -0.000 degrees.


On 11/13/06, Chris Weichenberger < cweich@cosy.sbg.ac.at> wrote:

  Dear PyMol users,

I am trying to set dihedral angles in a protein. Unfortunately, the
set_dihedral command is not documented, but it looks like it is the same
as the get_dihedral with an additional value for the angle to set. I tried
to set the dihedral angle for the protein crambin (PDB code 1CRN). First I
query the angle:

PyMOL>get_dihedral 21/n, 21/ca, 21/c, 22/n
  cmd.get_dihedral: 136.344 degrees.

I then assume that this command sets the dihedral angle to 0:

PyMOL>set_dihedral 21/n, 21/ca, 21/c, 22/n, 0.0
  SetDihedral: adjusted to 0.000

Therefore, it should be the case that the angle is 0, however, it is still
the old value:
PyMOL>get_dihedral 21/n, 21/ca, 21/c, 22/n
  cmd.get_dihedral: 136.344 degrees.

The graphics has changed but the molecule's overall topology still looks
like the original one. Also, repeating the above set_dihedral command
results in successively altered graphics, which contradicts my inuition
that setting a dihedral angle to the same fixed value should not result in
any changes at all. Has anyone played around with this command and can
report its proper usage? My ultimate goal is to write an animation that
folds a protein from a more or less linear chain to its final correct 3D
structure by interpolating dihedral angles.

I am running PyMol version 0.97.

Thanks for any help on this topic.


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