[phenixbb] neutron scattering table for specific metal isotope

Tim Gruene tg at shelx.uni-ac.gwdg.de
Thu Dec 4 05:46:09 PST 2014

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Dear Leif,

you can still make use of the X-ray structure if you use external
restraints - they can stabilise the non-H atom structure.

I don't understand why you need free variables for each of the
exchangeable hydrogens. If you were trying to determine the exchange
rate that might be a little over what crystallography can do for you.
Yet, you find a description of how you can do this from occupancy
refinement without the use of an abundant use of free variables in our
paper http://dx.doi.org/10.1107/S1600576713027659
There we made reasonable groups, but if you think you can justify it,
you could do the same for each hydrogen position.

I noticed that there are structures from neutron diffraction in the
PDB with hydrogen occupancies of 0.02 and the respective deuterium at
0.98 - I don't think such an accuracy is justifiable from
crystallographic data, this is merely overfitting the data.


On 12/04/2014 02:33 PM, Leif Hanson wrote:
> Tim, As I understand joint refinement (although Paul Langan and
> Marat Mustyakimov can give a better answer), the X-ray data are
> used to establish the non-H atom positions, and n0 data to
> establish H and D positions. From a practical standpoint, shelx was
> wonderful for defining the scattering factors of the atoms. But we
> had issues with the length of the input file since we had to create
> free variables for each of the exchangeable hydrogens. With more
> than 400 residues this got a little crazy. Leif
> On Thu, Dec 4, 2014 at 4:14 AM, Tim Gruene
> <tg at shelx.uni-ac.gwdg.de> wrote:
> Hi Maxime,
> you could use shelxl for refinement - it uses the values from the 
> Neutron Data Booklet for the most abundant isotopes, and you can
> mix them with your own scattering values without even looking at
> the code. You can even take into account incoherent contributions
> by adjusting the f' and f'' values on the SFAC command like NEUT 
> SFAC C H N O S D SFAC  FeX   0 0 0 0 0 0 0 0  4.20   0 0 11.220
> 1.23 56 SFAC Co
> if you have e.g. Fe-54
> If you want to have a joint refinement between X-ray and neutron
> data, I recommend using the X-ray structure by external restraints
> rather than mixing two different types of experiments. You won't
> e.g need to worry about different effective hydrogen bond lengths.
> Published restraints for hydrogen atoms to use with neutron data
> are available from my web-site, for ligands they can be generated
> by the grade-server.
> Regards, Tim
> On 12/03/2014 10:36 PM, Maxime Cuypers wrote:
>>>> Hello,
>>>> I would like to alter the neutron scattering table for 
>>>> phenix.refine so that it takes into account the correct
>>>> bcoherent value for the metal isotope present in my
>>>> structure. the difference is significative between the
>>>> natural occurence bcoh... i have been looking around in
>>>> chem_data but could not find the neutron scattering tables.
>>>> does anyone have any idea where to look please?
>>>> cheerios
>>>> _______________________________________________ phenixbb
>>>> mailing list phenixbb at phenix-online.org 
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- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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