[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




More information about the phenixbb mailing list