Hello Juergen,
since sigma is always positive, a negative I/sigI means that the measured
intensity is negative, hence I would refer you to the truncate reference
"On the treatment of negative intensity observations" by S. French and K.
Wilson, Acta Cryst (1978) A34, 517-525.
Why exactly -3 is chosen as a cut-off I cannot say, though, but it's better than
0 as cut-off, if I am not mistaken.
Cheers, Tim
On Tue, Feb 08, 2011 at 08:33:13AM -0500, Bosch, Juergen wrote:
> Hi Tim,
>
> could you write a bit more about this cutoff. I've been using the 0 cutoff for the longest time as it seemed to be much more stringent to report.
>
> Jürgen
>
> -
> Jürgen Bosch
> Johns Hopkins Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Phone: +1-410-614-4742
> Lab: +1-410-614-4894
> Fax: +1-410-955-2926
> http://web.mac.com/bosch_lab/<http://web.me.com/bosch_lab/>
>
> On Feb 8, 2011, at 7:45 AM, Tim Gruene wrote:
>
> Dear Simon,
>
> I don't know how to change the output written to the log-file (maybe with the
> TEST-card), but I wonder why you don't want to look at all of your data but only
> those with I/sigI > 0? XDS reports all reflections with I/sigI > -3 for a good
> reason.
>
> Cheers, Tim
>
> On Tue, Feb 08, 2011 at 12:17:35PM +0000, Simon Kolstoe wrote:
> Dear ccp4bb,
>
> I am quite a fan of XDS and have just upgraded to the latest version.
>
> Normally, to assess the quality of my data, I look at the tables in
> CORRECT.LP and especially the table "SUBSET OF INTENSITY DATA WITH
> SIGNAL/NOISE >= 0.0 AS FUNCTION OF RESOLUTION".
>
> However in my latest run I only get a single table for all the data
> i.e. for signal/noise >= -3.0. Is there a command I can put in my
> XDS.INP that will give me all the other tables or has the CORRECT.LP
> logfile been altered in the most recent version of XDS?
>
> (FYI my xds.inp obtained from the ESRF last week is copied below)
>
> Thanks,
>
> Simon
>
>
>
> !=== File Automaticaly generated by mxCuBE
> !=== X-Ray data collected at: ESRF_ID14-1
> !=== Detector type: ADSC Quantum Q210
> !=== Date: Fri Feb 04 03:39:09 2011
> !=== User comments:
>
> JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
> !JOB= DEFPIX XPLAN INTEGRATE CORRECT
>
> DATA_RANGE= 1 190
> SPOT_RANGE= 1 20
> SPOT_RANGE= 1 4
> !SPOT_RANGE= 187 190
> BACKGROUND_RANGE= 1 4
>
> SECONDS=60
> MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 6
> STRONG_PIXEL= 6.0
>
> OSCILLATION_RANGE= 1.000
> STARTING_ANGLE= 0.000
> STARTING_FRAME= 1
> X-RAY_WAVELENGTH= 0.93340
> NAME_TEMPLATE_OF_DATA_FRAMES= ./data/sk1_1_???.img
>
> !STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10
> !TOTAL_SPINDLE_ROTATION_RANGES= 60 180 10
>
> DETECTOR_DISTANCE= 298.55
> DETECTOR= ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000
> ORGX= 1014.79 ORGY= 1029.10
> NX= 2048 NY= 2048 QX= 0.10200 QY= 0.10200
> VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 7000 30000
>
> DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
> DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
> ROTATION_AXIS= 1.0 0.0 0.0
> INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0
> FRACTION_OF_POLARIZATION= 0.98
> POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
> !== Default value recommended
> !AIR= 0.00026895
>
> SPACE_GROUP_NUMBER= 0
> UNIT_CELL_CONSTANTS= 0 0 0 0 0 0
> INCLUDE_RESOLUTION_RANGE= 50.0 2.4
> RESOLUTION_SHELLS= 15.0 8.0 4.0 3.0 2.8 2.6 2.5 2.4
> FRIEDEL'S_LAW= FALSE
>
> !FRIEDEL'S_LAW= TRUE
> TRUSTED_REGION= 0 1.40
>
> REFINE(INTEGRATE)= BEAM ORIENTATION CELL
> !== Default value recommended
> !DELPHI= 3.000
> MAXIMUM_NUMBER_OF_PROCESSORS= 16
> !MAXIMUM_NUMBER_OF_JOBS= 16
>
> --
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> phone: +49 (0)551 39 22149
>
> GPG Key ID = A46BEE1A
>
>
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
GPG Key ID = A46BEE1A
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