From: Peter Freddolino (
Date: Sat Apr 02 2011 - 19:05:13 CDT

Hi Francesco,
Did you see the dihedral actually rotate in the vmd window?
Your procedure sounds incorrect in that, to get molefacture to recognize
a dihedral you need to have exactly two atoms selected, not four. When
you do this for two bonded atoms, you should see yellow spheres show up
highlighting other atoms involved in the dihedral, and then see the
atoms move as you move the dihedral slider. Does this happen?


On 04/02/2011 04:36 PM, Francesco Pietra wrote:
> Hi:
> I am unable to use molefacture correctly to change the value of a
> dihedral for the side chain of histidine, i.e. rotating the branch
> with the imidazole ring by some 90 degrees. I would be grateful for
> correcting my procedure with vmd 1.9beta1 starting from either a pdb
> or psf/pdb.
> (1) Load the molecule.
> (2) Molefacture.
> (3) select the residue HIS
> (4) Pick the four atoms for the dihedral.
> (5) Change the value of dihedral on the ruler.
> (6) File > Apply change to parent.
> whereby I find a molef_tmpfile_merge.xbgf where the dihedral is unchanged.
> Alternatively to (6)
> (7) Save .. pdb
> again no change to the dihedral.
> Sorry for posing such an uninteresting question.
> thanks for advice
> francesco pietra