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Dear Sam
If you look at the resolution shells you will see that they are rather different - if you used the same number of bins you would probably end up with much more similar results.
There are very few reflections at low resolution, changing the limit from 9A to 6A makes a *huge* difference
best wishes Graeme
________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Sam Tang [[log in to unmask]]
Sent: 28 April 2016 14:01
To: ccp4bb
Subject: [ccp4bb] Discrepancies between Scala and Aimless - innershell completeness
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Dear all
I guess I may have got stuck with an interesting scenario during data reduction. It happens that for a P1 native data set processed to 2.0 A, Aimless (via imosflm) returns the following statistics:
Overall InnerShell OuterShell
Low resolution limit 56.29 56.29 2.05
High resolution limit 2.00 8.94 2.00
Rmerge (within I+/I-) 0.075 0.054 0.119
Rmerge (all I+ and I-) 0.043 0.027 0.117
Rmeas (within I+/I-) 0.107 0.076 0.169
Rmeas (all I+ & I-) 0.061 0.038 0.166
Rpim (within I+/I-) 0.075 0.054 0.119
Rpim (all I+ & I-) 0.043 0.027 0.117
Rmerge in top intensity bin 0.057 - -
Total number of observations 104938 641 7753
Total number unique 53980 354 4056
Mean((I)/sd(I)) 8.0 11.5 3.9
Mn(I) half-set correlation CC(1/2) 0.990 0.995 0.960
Completeness 89.1 52.7 90.6
Multiplicity 1.9 1.8 1.9
The first thing that caught our attention was the low innershell completeness which was only 52.7%. Keeping the same input mtz, Scala (again via imosflm) returns the following:
Overall InnerShell OuterShell
Low resolution limit 56.29 56.29 2.11
High resolution limit 2.00 6.32 2.00
Rmerge 0.074 0.071 0.139
Rmerge in top intensity bin 0.056 - -
Rmeas (within I+/I-) 0.105 0.101 0.196
Rmeas (all I+ & I-) 0.059 0.040 0.206
Rpim (within I+/I-) 0.074 0.071 0.139
Rpim (all I+ & I-) 0.042 0.028 0.146
Fractional partial bias -0.045 -0.063 -0.093
Total number of observations 104951 2735 15336
Total number unique 53982 1460 7997
Mean((I)/sd(I)) 7.1 9.7 4.2
Mn(I) half-set correlation CC(1/2) 0.000 0.000 0.000
Completeness 89.1 75.9 90.7
Multiplicity 1.9 1.9 1.9
Innershell completeness jumps to 75.9% while overall and outershell completeness remain almost the same. Having asked crystallographers around no one has encountered this problem as usually they worry more about outershell completeness. Thus why is it so and would this obscure downstream calculations e.g. MR and refinement?
Thanks in advance!
PS - we have recently raised so many interesting (yet may be stupid) questions here as we have been dealing with quite a number of different data sets lately. We truly appreciate every efforts in replying and the advice received. Thank you for all these.
Regards
Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK
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