Re: [phenixbb] neutron scattering table for specific metal isotope

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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). Regards, Tim 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 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:

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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 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:

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> 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 [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb >

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