[phenixbb] neutron scattering table for specific metal isotope
Leif Hanson
leif.hanson at gmail.com
Thu Dec 4 18:18:06 PST 2014
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
On Thu, Dec 4, 2014 at 6:44 PM, Edward A. Berry <BerryE at upstate.edu> wrote:
> atom: C
> B: 10
> trial q : 0.10 0.20 0.30 0.40 0.50
> 0.60 0.70 0.80 0.90 1.00
> B_opt : 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 3.00 6.00 10.00
> CC(rho_ref,rho_opt) : 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00
> R(%) : 5.96 5.96 5.96 5.96 5.96
> 5.96 5.96 4.65 2.67 0.00
> CC(q,B): 0.75
>
> In cases where the CC(q,B) is poor like this, it seems to be because the B
> factor has pegged at 1.0, which it reaches at occupancy 0.7. Then as
> occupancy continues to decrease to 0.1, B remains the same, so CC(q,B) is
> low.
>
> And it is not surprising the CC(rho_ref,rho_opt) is very good in all
> cases, since you hardly change the shape of the map by dropping B by 9A^2.
> Note that if you set occupancy to 0.01 and didn't change the B-factor at
> all you would still get CC(rho_ref,rho_opt) =1. This doesn't mean we can't
> distinguish occupancy 0.01 from 1.0!
>
> It _is_ surprising that R also doesn't change as the occupancy drops from
> .7 to .1 with no compensation by B. This tells me there is some scaling
> going on in the calculation of R. In a real case with thousands of atoms,
> the scale would be fixed by the great majority of atoms at occupancy 1.0,
> and low occupancy for this atom would make a difference. So i suggest the R
> factor should be calculated without scaling. R going through the roof would
> then tell us that B is not successfully compensating for q. But I agree a
> 3-d plot of R vs B and q is the best way to show this.
> eab
>
>
>
> On 12/04/2014 05:29 PM, Pavel Afonine wrote:
>
>> Hello,
>>
>> 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
>>>
>>
>> sometimes numbers excite me! So this one caught my attention and I
>> decided to entertain myself.
>>
>> First off, an obvious statement: occupancy defines peak's height and
>> B-factor defines its shape. Therefore one cannot be entirely compensated
>> with the other.
>>
>> Now let's see if and how occupancy and B-factor are correlated. For this
>> let's take an atom and plot its electron density distribution with
>> occupancy q=1 and some B value; let's call this density rho_ref (reference
>> map). Then let's vary occupancy from 0.1 to 1.0 (with step 0.1) and for
>> each trial occupancy value find such B_opt that corresponding electron
>> density distribution fits rho_ref as good as possible; let's call it
>> rho_opt (map corresponding to optimal B_opt). In the end we will have ten
>> occupancy values and ten corresponding optimal B values so that we can
>> calculate the correlation between two sets of numbers (q, B_opt). In
>> addition let's calculate correlation and R-factor for rho_ref and rho_opt.
>>
>> We will repeat the numerical experiment defined above with:
>> a) different starting B values (10, 30, 50, 80),
>> b) different atoms H, C, S,
>> c) exact electron density distribution as well as its Fourier image of
>> 2A resolution.
>>
>> Attached script does it all in one go. Also it illustrates the beauty of
>> CCTBX that allows to do this so easily!
>>
>> Here are the numbers:
>>
>> Resolution: None (exact map)--------------------------
>> --------------------------------
>> atom: H
>> B: 10
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 1.00 2.00 3.00 5.00 6.00
>> 7.00 9.00 10.00
>> CC(rho_ref,rho_opt): 0.95 0.95 0.95 0.97 0.98 0.99 0.99
>> 1.00 1.00 1.00
>> R(%) : 34.94 34.94 34.94 28.30 23.09 14.83 11.36
>> 8.19 2.55 0.00
>> CC(q,B): 0.97
>> B: 30
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 4.00 7.00 11.00 14.00 17.00 21.00
>> 24.00 27.00 30.00
>> CC(rho_ref,rho_opt): 0.85 0.91 0.95 0.97 0.98 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 54.39 42.43 34.42 26.09 20.84 16.16 10.59
>> 6.81 3.29 0.00
>> CC(q,B): 1.00
>> B: 50
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 3.00 9.00 15.00 20.00 26.00 31.00 36.00
>> 41.00 45.00 50.00
>> CC(rho_ref,rho_opt): 0.84 0.91 0.95 0.97 0.98 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 55.33 42.14 32.91 26.59 20.01 15.15 10.72
>> 6.64 3.59 0.00
>> CC(q,B): 1.00
>> B: 80
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 8.00 18.00 27.00 35.00 43.00 51.00 59.00
>> 66.00 73.00 80.00
>> CC(rho_ref,rho_opt): 0.85 0.92 0.95 0.97 0.98 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 53.74 41.14 32.57 26.13 20.44 15.31 10.64
>> 6.86 3.32 0.00
>> CC(q,B): 1.00
>> atom: C
>> B: 10
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 2.00 3.00 4.00 5.00 6.00 7.00
>> 8.00 9.00 10.00
>> CC(rho_ref,rho_opt): 0.79 0.88 0.93 0.96 0.98 0.99 0.99
>> 1.00 1.00 1.00
>> R(%) : 62.77 49.83 39.70 31.37 24.32 18.23 12.89
>> 8.14 3.87 0.00
>> CC(q,B): 1.00
>> B: 30
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 4.00 7.00 10.00 13.00 16.00 19.00 21.00
>> 24.00 27.00 30.00
>> CC(rho_ref,rho_opt): 0.83 0.91 0.95 0.97 0.98 0.99 0.99
>> 1.00 1.00 1.00
>> R(%) : 56.51 43.81 34.49 27.06 20.84 15.45 12.21
>> 7.76 3.72 0.00
>> CC(q,B): 1.00
>> B: 50
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 6.00 12.00 17.00 22.00 27.00 32.00 36.00
>> 41.00 46.00 50.00
>> CC(rho_ref,rho_opt): 0.82 0.91 0.95 0.97 0.98 0.99 0.99
>> 1.00 1.00 1.00
>> R(%) : 57.64 42.58 33.79 26.68 20.63 15.32 11.47
>> 7.06 3.02 0.00
>> CC(q,B): 1.00
>> B: 80
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 11.00 20.00 28.00 36.00 44.00 52.00 59.00
>> 66.00 73.00 80.00
>> CC(rho_ref,rho_opt): 0.84 0.91 0.95 0.97 0.98 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 54.69 41.90 33.51 26.57 20.56 15.22 10.98
>> 7.06 3.41 0.00
>> CC(q,B): 1.00
>> atom: S
>> B: 10
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 2.00 3.00 4.00 5.00 6.00 7.00
>> 8.00 9.00 10.00
>> CC(rho_ref,rho_opt): 0.82 0.89 0.93 0.96 0.98 0.99 0.99
>> 1.00 1.00 1.00
>> R(%) : 59.32 47.29 38.28 30.75 24.21 18.39 13.15
>> 8.39 4.03 0.00
>> CC(q,B): 1.00
>> B: 30
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 4.00 8.00 11.00 14.00 17.00 19.00 22.00
>> 25.00 27.00 30.00
>> CC(rho_ref,rho_opt): 0.82 0.91 0.95 0.97 0.98 0.99 0.99
>> 1.00 1.00 1.00
>> R(%) : 57.49 42.56 33.98 26.75 20.48 16.72 11.57
>> 6.91 4.03 0.00
>> CC(q,B): 1.00
>> B: 50
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 8.00 13.00 19.00 23.00 28.00 33.00 37.00
>> 42.00 46.00 50.00
>> CC(rho_ref,rho_opt): 0.84 0.91 0.95 0.97 0.98 0.99 0.99
>> 1.00 1.00 1.00
>> R(%) : 54.25 43.18 32.90 27.17 20.88 15.31 11.27
>> 6.64 3.21 0.00
>> CC(q,B): 1.00
>> B: 80
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 13.00 22.00 30.00 38.00 46.00 53.00 60.00
>> 67.00 73.00 80.00
>> CC(rho_ref,rho_opt): 0.84 0.91 0.95 0.97 0.98 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 53.98 41.82 33.40 26.32 20.16 15.32 10.91
>> 6.83 3.57 0.00
>> CC(q,B): 1.00
>> Resolution: 2.0 ------------------------------
>> ----------------------------------------
>> atom: H
>> B: 10
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 1.00 1.00 1.00 1.00 1.00
>> 2.00 6.00 10.00
>> CC(rho_ref,rho_opt): 1.00 1.00 1.00 1.00 1.00 1.00 1.00
>> 1.00 1.00 1.00
>> R(%) : 5.93 5.93 5.93 5.93 5.93 5.93 5.93
>> 5.28 2.66 0.00
>> CC(q,B): 0.72
>> B: 30
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 1.00 1.00 4.00 10.00 16.00
>> 21.00 26.00 30.00
>> CC(rho_ref,rho_opt): 0.99 0.99 0.99 0.99 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 18.17 18.17 18.17 18.17 16.35 12.62 8.83
>> 5.66 2.50 0.00
>> CC(q,B): 0.95
>> B: 50
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 2.00 12.00 20.00 27.00 33.00
>> 39.00 45.00 50.00
>> CC(rho_ref,rho_opt): 0.97 0.97 0.97 0.98 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 27.44 27.44 26.91 21.35 16.76 12.70 9.30
>> 5.94 2.66 0.00
>> CC(q,B): 0.99
>> B: 80
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 6.00 20.00 31.00 41.00 50.00 58.00
>> 66.00 73.00 80.00
>> CC(rho_ref,rho_opt): 0.93 0.94 0.96 0.98 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 36.70 34.44 27.69 22.24 17.34 13.03 9.33
>> 5.80 2.84 0.00
>> CC(q,B): 1.00
>> atom: C
>> B: 10
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 1.00 1.00 1.00 1.00 1.00
>> 3.00 6.00 10.00
>> CC(rho_ref,rho_opt): 1.00 1.00 1.00 1.00 1.00 1.00 1.00
>> 1.00 1.00 1.00
>> R(%) : 5.96 5.96 5.96 5.96 5.96 5.96 5.96
>> 4.65 2.67 0.00
>> CC(q,B): 0.75
>> B: 30
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 1.00 1.00 5.00 11.00 16.00
>> 21.00 26.00 30.00
>> CC(rho_ref,rho_opt): 0.99 0.99 0.99 0.99 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 18.37 18.37 18.37 18.37 15.93 12.16 8.96
>> 5.75 2.54 0.00
>> CC(q,B): 0.95
>> B: 50
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 3.00 12.00 20.00 27.00 33.00
>> 39.00 45.00 50.00
>> CC(rho_ref,rho_opt): 0.97 0.97 0.97 0.98 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 27.82 27.82 26.75 21.70 17.07 12.95 9.48
>> 6.06 2.71 0.00
>> CC(q,B): 0.99
>> B: 80
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 7.00 21.00 32.00 41.00 50.00 58.00
>> 66.00 73.00 80.00
>> CC(rho_ref,rho_opt): 0.93 0.94 0.96 0.98 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 37.14 34.45 27.63 22.10 17.64 13.25 9.48
>> 5.90 2.88 0.00
>> CC(q,B): 1.00
>> atom: S
>> B: 10
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 1.00 1.00 1.00 1.00 1.00
>> 3.00 7.00 10.00
>> CC(rho_ref,rho_opt): 1.00 1.00 1.00 1.00 1.00 1.00 1.00
>> 1.00 1.00 1.00
>> R(%) : 5.88 5.88 5.88 5.88 5.88 5.88 5.88
>> 4.60 1.99 0.00
>> CC(q,B): 0.76
>> B: 30
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 1.00 1.00 6.00 11.00 17.00
>> 21.00 26.00 30.00
>> CC(rho_ref,rho_opt): 0.99 0.99 0.99 0.99 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 18.46 18.46 18.46 18.46 15.43 12.30 8.45
>> 5.84 2.59 0.00
>> CC(q,B): 0.96
>> B: 50
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 1.00 4.00 13.00 21.00 28.00 34.00
>> 40.00 45.00 50.00
>> CC(rho_ref,rho_opt): 0.97 0.97 0.97 0.98 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 28.30 28.30 26.67 21.63 16.92 12.75 9.18
>> 5.68 2.81 0.00
>> CC(q,B): 0.99
>> B: 80
>> trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>> 0.80 0.90 1.00
>> B_opt : 1.00 9.00 22.00 33.00 43.00 51.00 59.00
>> 66.00 73.00 80.00
>> CC(rho_ref,rho_opt): 0.93 0.94 0.96 0.98 0.99 0.99 1.00
>> 1.00 1.00 1.00
>> R(%) : 37.91 34.26 27.88 22.25 17.20 13.22 9.35
>> 6.10 2.99 0.00
>> CC(q,B): 0.99
>>
>> What we see here is:
>> - correlation of q and B is indeed approaches 100%;
>> - map correlation is greater than 90% in most cases except a few
>> corner cases;
>> - the last column in all tests is an obvious sanity check (CC=1, R=0
>> if exact B and q are used);
>> - R-factors are greater than zero except a trivial case. This is the
>> key that makes it possible to deconvolute q and B.
>>
>> All the best,
>> Pavel
>>
>>
>>
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