Consequences of Profile
Fitting Errors in Denzo
I reduced some mar 30cm data with Denzo, and things seemed to go OK. I am now having trouble with Scalepack. It seems to reject many reflections:
1 - count of observations deleted manually
2 - count of observations deleted due to zero sigma or profile test
3 - count of non-complete profiles (e.g. overloaded) observations
4 - count of observations deleted due to sigma cutoff
5 - count of observations deleted below low resolution limit,
6 - count of observations deleted above high resolution limit,
7 - count of partial observations
8 - count of fully recorded observations used in scaling
this line seems truncated:
\/
IP fitted, no o 2 1.0000 0.00 0 3520 0 0 0 0 886 1559
IP fitted, no o 3 0.9419 -0.27 0 3581 0 0 0 0 924 1503
IP fitted, no o 4 0.9741 0.30 0 3632 0 0 0 0 881 1551
IP fitted, no o 5 0.9717 0.67 0 3626 0 0 0 0 841 1500
IP fitted, no o 6 0.9535 0.79 0 3736 0 0 0 0 817 1450
IP fitted, no o 7 0.9241 0.78 0 3916 0 0 0 0 821 1364
...stuff deleted...
but yet gives a fairly good r-symms:
| Shell |
Lower |
Upper |
Average |
Average |
Norm. |
Linear |
Square |
limit
|
Angstrom |
I |
error |
stat. |
Chi**2 |
R-fac |
R-fac |
|
99.00 |
2.77 |
42346.7 |
1428.2 |
286.0 |
12.222 |
0.081 |
0.105 |
|
2.77 |
2.20 |
15502.0 |
625.4 |
312.4 |
12.300 |
0.113 |
0.143 |
|
2.20 |
1.92 |
9276.0 |
495.0 |
345.2 |
10.242 |
0.137 |
0.176 |
|
1.92 |
1.75 |
5322.0 |
418.9 |
357.7 |
5.829 |
0.142 |
0.189 |
|
1.75 |
1.62 |
4095.8 |
430.3 |
392.5 |
3.866 |
0.138 |
0.189 |
|
1.62 |
1.53 |
3472.9 |
483.1 |
416.1 |
2.413 |
0.138 |
0.191 |
|
1.53 |
1.45 |
3163.7 |
514.0 |
456.7 |
2.185 |
0.134 |
0.190 |
|
1.45 |
1.39 |
2780.1 |
500.9 |
453.3 |
1.522 |
0.126 |
0.207 |
|
1.39 |
1.33 |
2624.7 |
523.3 |
480.5 |
1.848 |
0.158 |
0.215 |
|
1.33 |
1.29 |
6305.7 |
882.4 |
733.4 |
6.906 |
0.241 |
0.363 |
|
|
|
|
|
|
|
|
All reflections |
17538.7 |
756.0 |
346.3 |
10.403 |
0.096 |
0.113 |
But there are no reflections with I/s
(I) less than 5:
| Shell |
I/Sigma in resolution shells: |
| Lower |
Upper |
No. of reflections with I / Sigma less than |
| limit |
limit |
0 |
1 |
2 |
3 |
5 |
10 |
20 |
>20 |
total |
| 99.00 |
2.77 |
0 |
0 |
0 |
0 |
5 |
143 |
1372 |
4655 |
6027 |
| 2.77 |
2.20 |
0 |
0 |
0 |
0 |
9 |
466 |
2152 |
3283 |
5435 |
| 2.20 |
1.92 |
0 |
0 |
0 |
0 |
36 |
804 |
2870 |
1756 |
4626 |
| 1.92 |
1.75 |
0 |
0 |
0 |
0 |
93 |
1201 |
2770 |
494 |
3264 |
| 1.75 |
1.62 |
0 |
0 |
0 |
0 |
106 |
1053 |
1817 |
80 |
1897 |
| 1.62 |
1.53 |
0 |
0 |
0 |
0 |
160 |
859 |
1079 |
1 |
1080 |
| 1.53 |
1.45 |
0 |
0 |
0 |
0 |
118 |
481 |
515 |
0 |
515 |
| 1.45 |
1.39 |
0 |
0 |
0 |
0 |
73 |
204 |
211 |
0 |
211 |
| 1.39 |
1.33 |
0 |
0 |
0 |
0 |
61 |
111 |
112 |
0 |
112 |
| 1.33 |
1.29 |
0 |
0 |
0 |
0 |
89 |
602 |
665 |
0 |
665 |
|
|
|
|
|
|
|
|
|
|
|
All hkl |
0 |
0 |
0 |
0 |
750 |
5924 |
13563 |
10269 |
23832 |
In the Scalepack output I get in the table for I/s
in resolution shells 0 reflections in the first five columns (I/s
0-5) i.e. I only get reflections with I/s
>= 5. I nowhere input a 5s
cutoff and looking through the manual the only explanation I found was the keyword weak level which has a default value of 5. On the other hand as I understand it, this only means that reflections <= 5s
are not used in refinement and as reference profiles. Is weak level the explanation (and should I rerun Denzo with an explicit value for weak level) or would you know any other reason for my missing data below 5s
?
Your problem comes from profile fitting radius not being set. You have to rerun Denzo .
weak level in Denzo has nothing to do with Scalepack Keyword
sigma cutoff
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