The only thing you can do is to move the detector in and collect higher
resolution. Then you can determine what the I/sigI ratio is for each of your
resolution shells and manually set the resolution limit once you run
HKL2000. As far as the R/Rfree values go, you will need to manually set the
weighting factor if you are using refmac. I have found that during the
initial rigid body refinement and the first few rounds of restrained
refinement, it works well if you keep the weighting factor low (0.01-0.9),
then as you go through a few rounds, gradually increase the weighting
factor. But keep in mind that as you increase the weighting factor, the
difference between R/Rfree will also increase.
----------------------------------------------------------------------------------
Greg Costakes
PhD Candidate
Department of Structural Biology
Purdue University
Hockmeyer Hall, Room 320
240 S. Martin Jischke Drive, West Lafayette, IN 47907
----------------------------------------------------------------------------------
--------------------------------------------------
From: "Mittal, Seema" <seema.mit...@umassmed.edu>
Sent: Friday, May 20, 2011 5:28 PM
To: <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] how to remove part of data with bad signal to noise ratio
Hi All,
I am currently working on a 3A resolution dataset. The scaled file shows
the following statistics (scroll down to the end of this email). It is
P212121 space group with R merge of 8.8%.
My question is : Is there a way to selectively use only the data with
I/Sigma value of 2 and more for refinement? And how do i achieve this
using refmac? I am aware that this would come at the cost of compromising
data completeness. Any suggestions/help would be greatly appreciated.
Thanks much,
Seema Mittal
Department of Biochemistry & Molecular Pharmacology
970L Lazare Research Building
University of Massachusetts Medical School
364 Plantation Street
Worcester, MA 01605
Shell I/Sigma in resolution shells:
Lower Upper % of of reflections with I / Sigma less than
limit limit 0 1 2 3 5 10 20
>20 total
50.00 6.46 2.0 3.8 5.3 6.2 7.6 12.5 34.3 65.0 99.3
6.46 5.13 0.7 2.2 3.9 5.3 8.2 15.7 36.6 63.4
100.0
5.13 4.48 1.3 2.8 4.0 5.8 9.3 13.8 27.3 72.7
100.0
4.48 4.07 0.7 1.7 4.0 5.4 7.9 13.9 35.4 64.1
99.5
4.07 3.78 1.8 3.6 5.1 6.9 11.8 20.8 49.6 47.3 96.9
3.78 3.56 1.5 3.8 6.7 8.7 13.3 26.7 65.4 30.8 96.2
3.56 3.38 0.8 3.2 7.1 8.9 12.9 31.1 76.6 20.0 96.6
3.38 3.23 2.0 4.8 8.1 14.8 23.4 44.8 84.7 12.7 97.5
3.23 3.11 4.1 9.2 13.8 18.4 29.6 51.0 86.0 11.0 96.9
3.11 3.00 2.4 8.6 13.9 18.8 30.6 53.9 92.4 4.5 96.9
All hkl 1.7 4.3 7.1 9.8 15.3 28.0 58.1 39.9
98.0
Shell Lower Upper Average Average Norm. Linear Square
limit Angstrom I error stat. Chi**2 R-fac R-fac
50.00 6.46 511.7 20.0 8.8 1.098 0.065 0.073
6.46 5.13 284.6 10.1 6.3 1.047 0.062 0.064
5.13 4.48 500.9 17.0 8.8 1.007 0.062 0.069
4.48 4.07 446.1 17.4 9.2 1.032 0.069 0.070
4.07 3.78 307.1 14.5 8.4 1.065 0.089 0.092
3.78 3.56 243.4 13.8 7.9 1.033 0.108 0.112
3.56 3.38 182.3 12.0 8.3 1.083 0.132 0.134
3.38 3.23 136.5 10.4 7.7 1.048 0.155 0.151
3.23 3.11 107.4 9.2 7.3 1.096 0.184 0.163
3.11 3.00 91.0 8.7 7.3 1.044 0.215 0.201
All reflections 287.7 13.5 8.0 1.055 0.088 0.082
