2,684
edits
Simulated-1g1c: Difference between revisions
Jump to navigation
Jump to search
→Towards better completeness: using the first two frames
| Line 637: | Line 637: | ||
EOF | EOF | ||
</pre> | </pre> | ||
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 === | ||