[phenixbb] neutron scattering table for specific metal isotope

Pavel Afonine pafonine at lbl.gov
Thu Dec 4 19:17:03 PST 2014

Hi Leif,

a few comments:

- occupancy, by definition, cannot be negative: "Occupancy is the 
fraction of molecules in the crystal in which a given atom occupies the 
position specified in the model" (where did I copy this from?.. anyway 
you get the idea!).

- We had a discussion with Marat about this at some point. If I remember 
correctly, files out of nCNS with negative occupancies are sort of 
temporary files or the likes, and there is a script that converts them 
into files that do not have negative occupancies and those files need to 
go to PDB deposition. This is my vague recollection..

- Rfactor is a global metric that is unlikely to be sensitive to a 
change in a parameter of one or a few atoms, unless these atoms 
represent a significant fraction of the whole structure (for example, if 
your structure consists of three atoms, and you vary an occupancy of one 
of thee atoms, then yes, Rfactor will "see" it).

- In phenix.refine exchangeable H/D sites always: a) have the same 
position, b) same B-factor, and c) their fractional (0<=q<=1) 
occupancies add up to one. If you see something different, please report 
a bug to me (a reproducible example that illustrates the problem).

All the best,

On 12/4/14 6:18 PM, Leif Hanson wrote:
> I have a question on these occupancies with respect to labile H atoms. 
> During the exchange process, we assume that the ratio of H to D at a 
> given atom will vary from 1 to 0 as deuteration increases. However, 
> since the scattering length varies from negative to positive (-0.3 to 
> 0.6 fm), does this enhance the ability to determine the occupancy? In 
> nCNS this shows up in the q column as -0.5 for H where 1 is a D. For 
> Phenix where both H and D for a given site are listed, the q values 
> vary from 0 to 1, although the fractional values don't necessarily add 
> to 1. I disremember whether the q value goes negative in Shelx.
> To follow on what Ed said, if one assumes that half of the atoms in a 
> structure are H, and 1/3 of those are labile, then up to 1/6 of the 
> structure has some variability for q. If one examines a His residue 
> and the scattering for one proton position is zero does this mean 
> nothing is there, or does it mean that it has 0.66 occupancy for His? 
> Would I really expect to see a change on R at this site with either no 
> proton, or 0.66 H?
> Leif

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