Re: [PyMOL] morphing between complexes

> unfortunately I've already tried that server and I've seen that also in
> that case, the ligand is stripped out.I obtain movies with only the
> protein movements. I don't know if i have problems with my pdbs:
> I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM
> indication, could be this a problem?

The server itself doesn't deal with heteroatoms, mostly because it makes 
dealing with the PDB even more of a nightmare than usual.  The underlying 
CNS input file will handle any ligand you want as long as you have the 
correct topology and parameter files (e.g. from Gerard Kleywegt's HIC-UP 
server).

I don't know of any program that will morph between *different* ligands, 
though.  You can cheat by using a dummy ligand that has the conserved 
core, and adding in the rest manually once you have the interpolation. 
For instance, to show ATP hydrolysis, you use ADP in both PDB files, and 
later re-insert the original ATP in place of the ADP in the first 
frame(s).  PyMOL makes this very easy.

-Nat