<div dir="ltr">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. <div>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?</div><div>Leif</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Dec 4, 2014 at 6:44 PM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""> atom: C<br>
B: 10<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 1.00 1.00 1.00 1.00 1.00 3.00 6.00 10.00<br>
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<br>
R(%) : 5.96 5.96 5.96 5.96 5.96 5.96 5.96 4.65 2.67 0.00<br>
CC(q,B): 0.75<br>
<br></span>
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.<br>
<br>
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!<br>
<br>
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.<span class="HOEnZb"><font color="#888888"><br>
eab</font></span><div><div class="h5"><br>
<br>
<br>
On 12/04/2014 05:29 PM, Pavel Afonine wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hello,<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I guess you are<br>
arguing that by using constraints there are more data available to<br>
refine B-values AND occupancy. You are probably aware that these to<br>
numbers are strongly correlated (>=90%!!) so that it is very tricky to<br>
get get reliable numbers anyhow<br>
</blockquote>
<br>
sometimes numbers excite me! So this one caught my attention and I decided to entertain myself.<br>
<br>
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.<br>
<br>
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.<br>
<br>
We will repeat the numerical experiment defined above with:<br>
a) different starting B values (10, 30, 50, 80),<br>
b) different atoms H, C, S,<br>
c) exact electron density distribution as well as its Fourier image of 2A resolution.<br>
<br>
Attached script does it all in one go. Also it illustrates the beauty of CCTBX that allows to do this so easily!<br>
<br>
Here are the numbers:<br>
<br>
Resolution: None (exact map)--------------------------<u></u>------------------------------<u></u>--<br>
atom: H<br>
B: 10<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 1.00 2.00 3.00 5.00 6.00 7.00 9.00 10.00<br>
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<br>
R(%) : 34.94 34.94 34.94 28.30 23.09 14.83 11.36 8.19 2.55 0.00<br>
CC(q,B): 0.97<br>
B: 30<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 4.00 7.00 11.00 14.00 17.00 21.00 24.00 27.00 30.00<br>
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<br>
R(%) : 54.39 42.43 34.42 26.09 20.84 16.16 10.59 6.81 3.29 0.00<br>
CC(q,B): 1.00<br>
B: 50<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 3.00 9.00 15.00 20.00 26.00 31.00 36.00 41.00 45.00 50.00<br>
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<br>
R(%) : 55.33 42.14 32.91 26.59 20.01 15.15 10.72 6.64 3.59 0.00<br>
CC(q,B): 1.00<br>
B: 80<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 8.00 18.00 27.00 35.00 43.00 51.00 59.00 66.00 73.00 80.00<br>
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<br>
R(%) : 53.74 41.14 32.57 26.13 20.44 15.31 10.64 6.86 3.32 0.00<br>
CC(q,B): 1.00<br>
atom: C<br>
B: 10<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00<br>
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<br>
R(%) : 62.77 49.83 39.70 31.37 24.32 18.23 12.89 8.14 3.87 0.00<br>
CC(q,B): 1.00<br>
B: 30<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 4.00 7.00 10.00 13.00 16.00 19.00 21.00 24.00 27.00 30.00<br>
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<br>
R(%) : 56.51 43.81 34.49 27.06 20.84 15.45 12.21 7.76 3.72 0.00<br>
CC(q,B): 1.00<br>
B: 50<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 6.00 12.00 17.00 22.00 27.00 32.00 36.00 41.00 46.00 50.00<br>
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<br>
R(%) : 57.64 42.58 33.79 26.68 20.63 15.32 11.47 7.06 3.02 0.00<br>
CC(q,B): 1.00<br>
B: 80<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 11.00 20.00 28.00 36.00 44.00 52.00 59.00 66.00 73.00 80.00<br>
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<br>
R(%) : 54.69 41.90 33.51 26.57 20.56 15.22 10.98 7.06 3.41 0.00<br>
CC(q,B): 1.00<br>
atom: S<br>
B: 10<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00<br>
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<br>
R(%) : 59.32 47.29 38.28 30.75 24.21 18.39 13.15 8.39 4.03 0.00<br>
CC(q,B): 1.00<br>
B: 30<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 4.00 8.00 11.00 14.00 17.00 19.00 22.00 25.00 27.00 30.00<br>
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<br>
R(%) : 57.49 42.56 33.98 26.75 20.48 16.72 11.57 6.91 4.03 0.00<br>
CC(q,B): 1.00<br>
B: 50<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 8.00 13.00 19.00 23.00 28.00 33.00 37.00 42.00 46.00 50.00<br>
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<br>
R(%) : 54.25 43.18 32.90 27.17 20.88 15.31 11.27 6.64 3.21 0.00<br>
CC(q,B): 1.00<br>
B: 80<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 13.00 22.00 30.00 38.00 46.00 53.00 60.00 67.00 73.00 80.00<br>
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<br>
R(%) : 53.98 41.82 33.40 26.32 20.16 15.32 10.91 6.83 3.57 0.00<br>
CC(q,B): 1.00<br>
Resolution: 2.0 ------------------------------<u></u>------------------------------<u></u>----------<br>
atom: H<br>
B: 10<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 1.00 1.00 1.00 1.00 1.00 2.00 6.00 10.00<br>
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<br>
R(%) : 5.93 5.93 5.93 5.93 5.93 5.93 5.93 5.28 2.66 0.00<br>
CC(q,B): 0.72<br>
B: 30<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 1.00 1.00 4.00 10.00 16.00 21.00 26.00 30.00<br>
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<br>
R(%) : 18.17 18.17 18.17 18.17 16.35 12.62 8.83 5.66 2.50 0.00<br>
CC(q,B): 0.95<br>
B: 50<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 2.00 12.00 20.00 27.00 33.00 39.00 45.00 50.00<br>
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<br>
R(%) : 27.44 27.44 26.91 21.35 16.76 12.70 9.30 5.94 2.66 0.00<br>
CC(q,B): 0.99<br>
B: 80<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 6.00 20.00 31.00 41.00 50.00 58.00 66.00 73.00 80.00<br>
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<br>
R(%) : 36.70 34.44 27.69 22.24 17.34 13.03 9.33 5.80 2.84 0.00<br>
CC(q,B): 1.00<br>
atom: C<br>
B: 10<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 1.00 1.00 1.00 1.00 1.00 3.00 6.00 10.00<br>
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<br>
R(%) : 5.96 5.96 5.96 5.96 5.96 5.96 5.96 4.65 2.67 0.00<br>
CC(q,B): 0.75<br>
B: 30<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 1.00 1.00 5.00 11.00 16.00 21.00 26.00 30.00<br>
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<br>
R(%) : 18.37 18.37 18.37 18.37 15.93 12.16 8.96 5.75 2.54 0.00<br>
CC(q,B): 0.95<br>
B: 50<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 3.00 12.00 20.00 27.00 33.00 39.00 45.00 50.00<br>
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<br>
R(%) : 27.82 27.82 26.75 21.70 17.07 12.95 9.48 6.06 2.71 0.00<br>
CC(q,B): 0.99<br>
B: 80<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 7.00 21.00 32.00 41.00 50.00 58.00 66.00 73.00 80.00<br>
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<br>
R(%) : 37.14 34.45 27.63 22.10 17.64 13.25 9.48 5.90 2.88 0.00<br>
CC(q,B): 1.00<br>
atom: S<br>
B: 10<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 1.00 1.00 1.00 1.00 1.00 3.00 7.00 10.00<br>
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<br>
R(%) : 5.88 5.88 5.88 5.88 5.88 5.88 5.88 4.60 1.99 0.00<br>
CC(q,B): 0.76<br>
B: 30<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 1.00 1.00 6.00 11.00 17.00 21.00 26.00 30.00<br>
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<br>
R(%) : 18.46 18.46 18.46 18.46 15.43 12.30 8.45 5.84 2.59 0.00<br>
CC(q,B): 0.96<br>
B: 50<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 1.00 4.00 13.00 21.00 28.00 34.00 40.00 45.00 50.00<br>
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<br>
R(%) : 28.30 28.30 26.67 21.63 16.92 12.75 9.18 5.68 2.81 0.00<br>
CC(q,B): 0.99<br>
B: 80<br>
trial q : 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00<br>
B_opt : 1.00 9.00 22.00 33.00 43.00 51.00 59.00 66.00 73.00 80.00<br>
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<br>
R(%) : 37.91 34.26 27.88 22.25 17.20 13.22 9.35 6.10 2.99 0.00<br>
CC(q,B): 0.99<br>
<br>
What we see here is:<br>
- correlation of q and B is indeed approaches 100%;<br>
- map correlation is greater than 90% in most cases except a few corner cases;<br>
- the last column in all tests is an obvious sanity check (CC=1, R=0 if exact B and q are used);<br>
- R-factors are greater than zero except a trivial case. This is the key that makes it possible to deconvolute q and B.<br>
<br>
All the best,<br>
Pavel<br>
<br>
<br>
<br></div></div><span class="">
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</span></blockquote><div class="HOEnZb"><div class="h5">
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