[phenixbb] neutron scattering table for specific metal isotope

Leif Hanson leif.hanson at gmail.com
Thu Dec 4 06:12:11 PST 2014


Tim,
Let me see if I understand this process flow properly. Let us assume that
we have measured two datasets from the same crystal, one neutron, one X-ray
(neutron always measured first). I use shelx to refine the x-ray structure
to 'stability'. I then use that structure and the input cards from X-ray
structure to solve the neutron structure. This is normally what we do. We
do not allow the structure to move after X-ray positional refinement,
refining only b-factors and occupancies. The primary activity at this point
is resolving protonation and water orientation. There are some issues with
this strategy (what about X-radiation damage to acidic residues and water
molecules?), but it has been reliable to this point. The features for
neutron refinement in Phenix as I understand it position the H and D atoms
at the end of each major cycle, then complete the b and q refinement. Does
this differ from what you are suggesting?
I agree that the 0.98 occupancy should be considered unity, although it
might be valid for Julian Chen's crambin structure.
Leif

On Thu, Dec 4, 2014 at 8:46 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de> wrote:

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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.
>
> Cheers,
> Tim
>
> 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
> >>>> http://phenix-online.org/mailman/listinfo/phenixbb
> >>>>
> >
> >> _______________________________________________ phenixbb mailing
> >> list phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >>
> >
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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