[phenixbb] PDB deposition
Kay Diederichs
kay.diederichs at uni-konstanz.de
Mon May 27 14:17:33 PDT 2013
Dear Phenix developers,
the following questions came up today, during an attempt to answer the
questions that the PDB asks at deposition time:
a) For Bulk solvent modeling, what should be given as value for K sol
and B sol ? My understanding is that the new solvent model does no
longer result in these values; the table is
Total model structure factor:
F_model = k_total * (F_calc + k_mask * F_mask)
k_total = k_isotropic * k_anisotropic
Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso
kani kmask
37.014-13.525 85.34 95 4 7.2146 38.755 318.867 0.937
1.000 0.300
13.240-10.663 91.82 91 10 7.1453 40.328 328.027 0.901
1.000 0.309
10.640-8.570 93.27 202 6 7.4011 38.069 318.901 0.905
1.002 0.310
8.548-6.875 95.70 380 21 7.2679 31.166 258.647 0.901
1.000 0.309
6.871-5.523 95.40 731 36 7.1964 29.485 241.669 0.908
1.001 0.302
5.520-4.439 90.49 1347 61 7.3445 39.504 329.514 0.934
1.001 0.281
4.438-3.568 92.52 2610 150 7.3166 41.793 347.063 0.961
1.000 0.280
3.567-2.867 94.10 5191 231 7.2983 33.593 278.704 0.965
1.000 0.024
2.867-2.304 92.97 9835 476 7.3098 23.922 198.755 0.984
1.000 0.000
2.304-1.852 92.81 18869 947 7.3097 18.746 155.751 1.053
1.000 0.000
1.852-1.488 90.33 35341 1797 7.3288 10.914 90.931 1.035
0.999 0.000
1.488-1.196 86.49 64979 3561 7.2975 6.848 56.810 1.028
0.998 0.000
1.196-1.081 53.28 29672 1567 7.1776 5.351 43.737 0.986
1.000 0.000
Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
k_overall=1.0149 b_overall=-0.0072
So what can we do here?
b) there is the question about Overall Anisotropic values B11; B22; B33;
B12; B13; B23....
but the logfile offers
overall anisotropic scale matrix:
V0: -0.0214,0.0415,-0.0249,0.0006,-0.0515,-0.0161
V1: -0.0055,-0.0022,0.0080,-0.0001,-0.0020,0.0011
So which of these should be given?
I've tried to locate the information about these two questions in the
documentation, but it seems I missed it!
thanks,
Kay
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