[MMTK] bad lysine protonation

Robert Jorissen robjorissen at yahoo.com.au
Thu Sep 4 12:13:15 UTC 2008


G'day Konrad

> 
> > 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?

I am using the latest Windows installation of MMTK for Python 2.5
which is pywin32-211.win32-py2.5.exe, plus Numeric-23.8.2 and ScientificPython-2.7.8. I also have NumPy and SciPy on my home
machine. (I probably have a similar set-up for my work machine
which gives me the same results as the script does on my computer
at home.) With the additional code I mentioned (CYS->CYX), the PDB
file produced is exactly the same as yours, but without it, I get
the cysteine HG atoms, plus some weird stuff at the end of the PDB
output.

> 
> 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.
> 
Changing CYS to CYX in the PDB file (using sed) prior to
reading it in using the line:
configuration = MyPDBConfiguration('1B2F_CYX.pdb')
also leads to a presumed disulfide bond being created.
But without it, I do not have the CYS -> CYX change occurring
automatically, not on the computers I put MMTK on.


> Konrad.
> --
> ---------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------

Thanks again for your help,

Rob Jorissen
Ludwig Institute for Cancer Research, Melbourne branch



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