[phenixbb] neutron scattering table for specific metal isotope

Tim Gruene tg at shelx.uni-ac.gwdg.de
Thu Dec 4 06:35:44 PST 2014

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Hi Leif,

the procedure you suggest, i.e. to fix the coordinates from the
refinement against X-ray data, is of course possible in shelxl. This
means you use the X-ray structure as CONstraint.

I would, though, prefer to generate REstraints with prosmart and
transcribe its output into shelx format - which is not too difficult.
This way you allow room for differences between X-ray and neutron
diffractions that we may simply not be aware of (or are aware of like
the radiation damage you mention).

When I refined against neutron data, I did not consider it necessary
to take the X-ray structure into account at all. I guess you are
arguing that by using constraints there are more data available to
refine B-values AND occupancy. You are probably aware that these to
numbers are strongly correlated (>=90%!!) so that it is very tricky to
get get reliable numbers anyhow (see e.g.
http://www.sciencemag.org/content/346/6207/352). (Very) high
resolution data should help to reduce the CC, but I would be cautious
to think that mathematically increasing the data to parameter ratio by
using constraints improves the CC. But I never tried - shelxl prints
the highest CC values if you use 'MORE 3' and L.S. as minimisation
method (instead of CGLS).


On 12/04/2014 03:12 PM, Leif Hanson wrote:
> 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:
> 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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