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