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
signature.asc
Description: Digital signature
