[phenixbb] PDB deposition

[Pavel Afonine]

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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