Simulated-1g1c: Difference between revisions

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Using the default (see above) phenix.refine job, I obtain against the [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/1g1c/xds-simulated-1g1c-F-2frames.mtz MTZ file with amplitudes]:
Start R-work = 0.3434, R-free = 0.3540
Final R-work = 0.2209, R-free = 0.2479
and against the [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/1g1c/xds-simulated-1g1c-I-2frames.mtz MTZ file with intensities]
Start R-work = 0.3492, R-free = 0.3606
Final R-work = 0.2244, R-free = 0.2504
so: better R-free is obtained from better data.
The statistics from SHELXD and SHELXE don't look better - they were already quite good with a single frame per dataset. The statistics printed by SHELXE (for the correct hand) are:
...
<wt> = 0.300, Contrast = 0.591, Connect. = 0.740 for dens.mod. cycle 50
Estimated mean FOM and mapCC as a function of resolution
d    inf - 3.98 - 3.13 - 2.72 - 2.47 - 2.29 - 2.15 - 2.04 - 1.95 - 1.87 - 1.81
<FOM>  0.601  0.606  0.590  0.570  0.538  0.542  0.521  0.509  0.529  0.498
<mapCC> 0.841  0.813  0.811  0.786  0.763  0.744  0.727  0.740  0.761  0.722
N        2289  2303  2334  2245  2289  2330  2299  2297  2429  2046
Estimated mean FOM = 0.551  Pseudo-free CC = 59.42 %
...
Site    x      y      z  h(sig) near old  near new
  1  0.7375  0.6996  0.1537  20.4  1/0.06  2/15.05 6/21.38 3/21.54 5/22.03
  2  0.7676  0.7231  0.3419  18.8  3/0.13  5/12.15 1/15.05 3/21.34 4/22.43
  3  0.5967  0.4904 -0.0067  17.2  4/0.10  4/4.90 6/4.94 2/21.34 1/21.54
  4  0.5269  0.5194 -0.0498  17.1  2/0.05  3/4.90 6/7.85 2/22.43 1/22.96
  5  0.4857  0.6896  0.4039  -4.8  3/12.04  2/12.15 1/22.03 3/22.55 2/22.85
  6  0.5158  0.4788  0.0406  4.7  5/1.45  3/4.94 4/7.85 1/21.38 5/23.30
Using these four sites (and standard parameters otherwise, I obtained from the [http://cci.lbl.gov/cctbx/phase_o_phrenia.html cctbx - Phase-O-Phrenia server] the following
Plot of relative peak heights:
    |*
    |*
    |*
    |*
    |**
    |**
    |***
    |****
    |******
    |************
    |********************
    |*****************************
    |*********************************
    |***************************************
    |************************************************
    |************************************************************
    |************************************************************
    |************************************************************
    |************************************************************
    |************************************************************
    -------------------------------------------------------------
Peak list:
  Relative
  height  Fractional coordinates
    97.8  0.01982  0.49860 -0.00250
    80.2  0.17362  0.71758  0.83714
    71.5  0.02405  0.53538  0.48365
    63.9  -0.00511  0.07044  0.50289
    62.1  0.02410  0.94827  0.48807
    61.3  0.16922  0.28605  0.15985
    56.3  0.12047  0.50910  0.43665
    55.9  0.21871  0.26331  0.30008
    55.7  0.10931  0.47245  0.53659
    53.0  0.22211  0.23746  0.39503
    52.9  0.03449 -0.00661  0.98264  <------ this peak is close to the origin
    52.5  0.06905  0.02372  0.05632  <------ this one, too
    ...
so the strongest peak corresponds to the translation of molecules (0,0.5,0) but the origin peak is at 1/2 of that size, which appears significant. (I cannot interpret the plot of relative peak heights, though <big>☹</big>)


=== Why this is difficult to solve with SAD phasing ===
=== Why this is difficult to solve with SAD phasing ===
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