[MMTK] bad lysine protonation

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed Sep 3 13:37:55 UTC 2008

On 03.09.2008, at 05:16, Robert Jorissen wrote:

> Your suggestion does indeed fix my problem with the lysine residue.  
> Thank you.
> However, in my case, I did not have the cysteines changed  
> automatically from CYS (no disulfide bond) to CYX (disulfide bond).  
> After the line:

That sounds rather strange, given that the very same script does  
create CYX when I run it on my machine. Which versions of MMTK and  
ScientificPython are you using? Are there any other differences  
between the PDB file you produce (with the hydrogens) and the one I  
sent you?

And just to be sure: where did you check if CYS was transformed into  
CYX? It has to be done in the PDB file, not in the PDBConfiguration  
object. That transformation happens after the MMTK objects have been  
created from the PDB data. In fact, MMTK first makes the protein "as  
is" (with cystines), then checks for S-S distances in the right  
range, and replaces the cystine residues by cysteines where required  
to add the bond.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr

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