[phenixbb] neutron scattering table for specific metal isotope
tg at shelx.uni-ac.gwdg.de
Thu Dec 4 05:46:09 PST 2014
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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
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:
>>>> 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?
>>>> _______________________________________________ phenixbb
>>>> mailing list phenixbb at phenix-online.org
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>> list phenixbb at phenix-online.org
Dr Tim Gruene
Institut fuer anorganische Chemie
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