proton addition to high atomic resolution crystal structure

Kevin Karplus karplus at
Thu Jan 22 22:43:52 EST 2004

In article <qg2Ob.1284$np6.764 at>, George Elkins wrote:
> "Oscar Hur" <oscarhur at> wrote 
>> I have a batch of high resolution/atomic resolution X ray crystal
>> structure PDB files.  I want to look at the proton position and geometry
>> on the proteins.  I heard that there are softwares that can add protons
>> computationally to the high resolution/atomic resolution crystal
>> structures.  Any recommendation?
> If you want the protons, why not just use protein structures derived from
> NMR spectroscopy?

Oscar is working with me, so perhaps I can explain.  We were looking
for rules we could use to convert hydrogen distance restraints into
constraints on the corresponding heavy atoms.  

In crystallographic data, the atoms that are not well-located are
missing from the PDB files (or have high B factors), while in NMR
files, one has to infer that an atom is not well-located by looking
for how much its position varies in different NMR models.  This makes
doing statistical work with large numbers of models much more
difficult with NMR data.

We felt that it was easier to add hydrogens to Xray structures to get
high-resolution data on heavy atoms and hydrogens than to create a clean
subset of NMR data.

There is also a lot more data available from high-resolution X-ray
experiments, making the statistics more robust.

Kevin Karplus 	karplus at
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
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