[phenixbb] neutron scattering table for specific metal isotope
Dale Tronrud
detBB at daletronrud.com
Thu Dec 4 15:16:00 PST 2014
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
You haven't quite finished the job Pavel. In your test you are
always starting with an atom with occupancy of 1. Those atoms we
usually know have an occupancy of 1 so we constrain to that value.
The real question come up with the occupancy is less than one, but we
don't know either the B or the Occ.
Then you need to plot R value in 2-D as both Occ and B are varied.
The correlation we all talk of is due to a diagonal line of minimal R
in that plot. Since there are a bunch of different combinations of B
and Occ that give similar fit we end up with a relationship between
the possible values. Certainly when you change EITHER Occ or B alone
(as you have done here) you see a change to the fit to the data.
Use your CCTBX wizardry to show us the 2-D plot!
Dale Tronrud
On 12/4/2014 2:29 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
>
>
>
> _______________________________________________ phenixbb mailing
> list phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.22 (MingW32)
iEYEARECAAYFAlSA6zAACgkQU5C0gGfAG13hmQCffgQcmT94H12EDsNIE6UTdcx/
wFUAn0RWRfce/o8nQXZpKDowZkhS+1Vi
=2mMN
-----END PGP SIGNATURE-----
More information about the phenixbb
mailing list