Hi Kay, there is no single number to report. The new scaling model (not really new, actually, as we switched to using it in April 2012) uses either exponential or polynomial model for overall anisotropic scaling (choice is dynamic depending which one works better) and bulk-solvent mask scale is resolution dependent and not exp. Details are described in our paper: http://journals.iucr.org/d/issues/2013/04/00/dz5273/index.html I recall a few people asked me the same question, and also I recall PDB deposition wasn't a problem. Can you just not report ksol, Bsol and Bcart as non-applicable? Pavel On 5/27/13 2:17 PM, Kay Diederichs wrote:
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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