Hi Joel,

The trick is to have all the atoms through out the morph in every single pdb.
Thus, pdb1 needs to have ligands from pdb2 and pdb3 and so forth.
Move the non-bound ligands out of the binding site for every pdb.
If you run Rigimol now you will see the ligands, in turn, bind to the binding site.

If the ligands are derivatives of each other (e.g. ATP -> ADP + P) you have a diffent situation.

Then the ligand should be broken down into the respective fragments in all 3 pdbs. Rename the molecules to the same through out the 3 pdb, but use the specific coordinates for every atom in the pdbs.
The trick here, is to exclude the ligand components from the refinement step in Rigimol, otherwise it will explode in this sted. Grep it out the pdb after rigimol and put it in a separate pdb that is loaded together with the rest in pymol.

It is a while ago since I worked with Rigimol, so this a very crude despription, but I hope this could be to some help to you.

For inspiration you could look at one of the morphs I have done in Rigimol here:
It shows the SERCA CA2+-ATPase pumping calciums.

Good luck!

Jesper L. Karlsen
Scientific Computing
Centre for Structural Biology
Department of Molecular Biology
University of Aarhus
Gustav Wieds Vej 10C
8000 Aarhus C

Phone: +45 8942 5268
E-mail: jelka@bioxray.au.dk

Joel Tyndall wrote:

Hi folks,


I was wondering if anyone can help. I have made some nice morphs using rigimol/ipymol based on Warren’s examples (Thanks Warren). I was wondering if anyone has any scripts to do the following.


I have generated a morph with two structures with two different ligands  where there is a conformational change of the protein between the two ligands. There exists an intermediate structure which I would like to include also. How can I include this i.e. I want to morph from 1 to 2 then to 3 and show the ligands (changing) as well?


Many thanks for any help in advance.





Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand                   


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