Re: [PyMOL] Rigimol/ipymol

[Jesper L. K. <je...@bi...>]

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:
http://www.pumpkin.au.dk/research/picturevideo-gallery/
It shows the SERCA CA2+-ATPase pumping calciums.

Good luck!

Jesper

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: je...@bi...



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
>
>  
>
> _________________________________
>
> Joel Tyndall, PhD
>
> Senior Lecturer in Medicinal Chemistry
> National School of Pharmacy
> University of Otago
> PO Box 56 Dunedin 9054
> New Zealand                   
> http://www.researcherid.com/rid/C-2803-2008
>
> Pukeka Matua
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 56 Otepoti 9054
> Aotearoa
>
> Ph / Waea               +64 3 4797293
> Fax / Waeawhakaahua     +64 3 4797034
>
>  
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...