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

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

Leif Hanson