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Dear Daniel,
could be, especially if you expect that many copies in the unit cell.
The third peak looks suspiciously close to the origin peak +(0,1,0) and
could be a ripple peak. I would suggest that you calculate a
self-rotation function and a Patterson map (with peak-search) at rather
low resolution (~5-6 A). The self-rotation function should indicate the
presence of any NCS rotation, the Patterson map should indicate any NCS
translation. I find it also very instructive to look at the Patterson
map in a graphics program like Coot to get an impression of the clarity
and shape of the peaks. A Patterson map covering the whole unit cell is
a bit easier to look at. Maybe, these additional informations help you
to confirm any potential MR solution.
Good luck,
Dirk.
Daniel Adams wrote:
Dear bb,
I am trying to figure out SRF for P1 space group dataset using Molrep.
The programme indicates the presence of pseudotranlation however the peaks
heights are confusing me...
The output of MOLREP is follows:
-- Fobs --
-------------
Fobs: resolution : 29.89 2.80
Completeness of Fobs : 0.980
B_overall of Fobs : 36.021
Optical resolution : 2.005
Anisotropic distribution of Structure Factors:
Ratio of Eigen values : 0.9627 0.4958 1.0000
-------------
Resolution will be used : 29.89 4.00
-------------
INFO: anisothermal correction of Fobs ---
--- Check Patterson for pseudo-translation ---
PST_limit : 0.125 of origin peak
INFO: pseudo-translation was detected.
Origin Patterson peak: P,P/sig : 8748.844 140.071
1 Patterson. peak : p,P/sig : 1694.444 27.128
2 Patterson peak : P,P/sig : 809.574 12.961
3 Patterson peak : P,P/sig : 649.761 10.403
Peak 1: trans.vector /ort/ : 11.342 0.000
0.000
trans.vector /frac/: 0.152 0.000
0.000
Peak 2: trans.vector /ort/ : 22.779 0.000
0.000
trans.vector /frac/: 0.306 0.000
0.000
Peak 3: trans.vector /ort/ : 2.457 85.961
0.617
trans.vector /frac/: 0.037 0.948
0.006
INFO: use keyword: "PST".
Sol_ Space group : P 1
Sol_ No: 1 Sett: 1
Sol_ Cell: 74.540 90.930 120.610 109.23 110.92 90.03
Sol_--- Self Rotation function ---
Sol_
--- anisothermal correction of Fobs ---
Radius of integration : 35.00
Resmin,Resmax : 29.89 4.00
--- rfcoef for Fobs. ---
distance limit : 2.000 / grad /
Number of RF peaks : 30
theta phi chi alpha beta gamma
Rf Rf/sigma
Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 295.0
21.24
Sol_RF 2 172.27 -88.17 180.00 91.83 15.45 88.17 159.1
11.46
Sol_RF 3 97.66 90.33 180.00 270.33 164.69 269.67 137.9
9.93
Sol_RF 4 90.00 -179.40 180.00 313.80 180.00 132.60 121.4
8.74
Sol_RF 5 163.40 -25.19 180.00 154.81 33.19 25.19 118.4
8.53
Sol_RF 6 142.86 -89.96 180.00 90.04 74.28 89.96 98.14
7.07
Sol_RF 7 162.97 -90.08 180.00 89.92 34.05 90.08 97.46
7.02
Sol_RF 8 148.91 -90.06 180.00 89.94 62.18 90.06 96.48
6.95
Sol_RF 9 95.89 -89.67 180.00 90.33 168.23 89.67 95.26
6.86
Sol_RF 10 180.00 0.00 180.00 180.00 0.00 0.00 94.75
6.82
Sol_RF 11 173.15 91.79 180.00 271.79 13.70 268.21 94.34
6.79
Sol_RF 12 157.43 91.67 179.98 271.67 45.14 268.33 94.29
6.79
Sol_RF 13 89.66 1.71 28.37 271.79 28.37 88.38 94.23
6.78
Sol_RF 14 90.34 -178.29 28.37 91.62 28.37 268.21 94.23
6.78
Sol_RF 15 135.06 -89.96 180.00 90.04 89.88 89.96 93.13
6.70
Sol_RF 16 121.29 89.44 180.00 269.44 117.43 270.56 93.11
6.70
Sol_RF 17 165.19 90.06 180.00 270.06 29.61 269.94 92.96
6.69
Sol_RF 18 106.06 -89.84 180.00 90.16 147.88 89.84 92.83
6.68
Sol_RF 19 88.53 0.14 46.03 270.76 46.02 90.49 92.34
6.65
Sol_RF 20 91.47 -179.86 46.03 89.51 46.02 269.24 92.34
6.65
Sol_RF 21 112.75 -89.54 180.00 90.46 134.51 89.54 92.16
6.64
Sol_RF 22 109.99 90.00 180.00 270.00 140.01 270.00 91.80
6.61
Sol_RF 23 89.89 -179.85 120.54 90.34 120.54 270.04 91.11
6.56
Sol_RF 24 90.11 0.15 120.54 269.96 120.54 89.66 91.11
6.56
Sol_RF 25 90.00 0.10 155.48 270.11 155.48 89.90 90.13
6.49
Sol_RF 26 90.00 -179.90 155.48 90.10 155.48 269.89 90.13
6.49
Sol_RF 27 150.73 89.77 180.00 269.77 58.54 270.23 89.47
6.44
Sol_RF 28 115.82 89.94 180.00 269.94 128.37 270.06 89.27
6.43
Sol_RF 29 135.80 90.11 180.00 270.11 88.39 269.89 88.69
6.38
Sol_RF 30 90.24 -0.07 65.22 269.77 65.22 89.91 88.37
6.36
My question is:
1. Is there really a three pseudotranslationally related molecules ?
my asymmetric unit have 12 molecules (50% solvent content) and
biochemically data indicates either hexameric or tetrameric assembly.
2. What is the best way to figure out the pseudotranslation ?
3. When I do SRF for data containing PST, should I expect SRF for all
molecules or for 1 molecule. I understand that orientation of PST related
molecules should be same.
Thanks in advance.
Cheers
Dan
--
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
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