On Jan 16, 2013, at 2:19 PM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote:
> -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Sebastiano, > > if the output of GO.COM produces an mtz-file you can use for phasing > or refinement, I am very confident there is a scaling step involved. Sorry, my bad. I meant there's no XSCALE nor scala that has been run. CORRECT does the scaling. > This might also be an explanation for the discrepancy you point out: > With FRIEDEL'S_LAW=TRUE the statistics which affects the rejection of > outliers would have more reflections within each group of symmetry > related reflections and hence a greater spread which might lead to the > rejection of some of the classes. But this is a mere guess. The way I performed the two runs was by running CORRECT step of XDS followed by XDSCONV, f2mtz and cad. When working with the FRIEDEL'S_LAW flag on, CORRECT outputs F(+), F(-) but also merged F. I was expecting those were merged identically to the case in which FRIEDEL'S_LAW is off. But maybe your point is correct. Thanks, s > Cheers, > Tim > > On 01/16/2013 02:03 PM, Sebastiano Pasqualato wrote: >> >> Thanks to Kay and Tim or the feedback. >> >> The reason I wanted to get statistics from the CORRECT step of XDS >> is that I have refined a structure using the mtz output by the >> GO.COM automatic reduction routine of SLS beamline PXIII, which >> does not involve a scaling step (I discovered recently). I was >> willing to have the integration statistics of the reflection file I >> used in the refinement's high resolution bin. I will definitely >> give xprep a try. >> >> Another question that raised by looking deeper into their automatic >> procedure (thanks Meitian for the help) is that when integrating >> with XDS CORRECT keeping the FRIEDEL'S_LAW=TRUE or =FALSE I get a >> different number of reflections in the final mtz. >> >> In my case, if I run the same XDS.INP script and change only the >> FRIEDEL'S_LAW flag, I obtain: >> >> >> =TRUE: 11551 reflections >> >> * Resolution Range : >> >> 0.00043 0.11138 ( 48.225 - 2.996 A ) >> >> * Sort Order : >> >> 1 2 3 0 0 >> >> * Space group = 'P 3 2 1' (number 150) >> >> >> >> OVERALL FILE STATISTICS for resolution range 0.000 - 0.111 >> ======================= >> >> >> Col Sort Min Max Num % Mean Mean Resolution >> Type Column num order Missing complete abs. >> Low High label >> >> 1 ASC 0 29 0 100.00 13.7 13.7 48.22 3.00 >> H H 2 NONE 0 16 0 100.00 4.7 4.7 48.22 >> 3.00 H K 3 NONE -32 32 0 100.00 0.5 12.2 >> 48.22 3.00 H L 4 NONE 1.4 292.0 0 100.00 19.40 >> 19.40 48.22 3.00 F FP 5 NONE 0.1 4.3 0 100.00 >> 0.70 0.70 48.22 3.00 Q SIGFP 6 NONE 0.0 1.0 0 >> 100.00 0.95 0.95 48.22 3.00 I FreeRflag >> >> >> No. of reflections used in FILE STATISTICS 11551 >> >> >> =FALSE: 11643 reflections >> >> * Cell Dimensions : (obsolete - refer to dataset cell dimensions >> above) >> >> 100.5450 100.5450 96.4500 90.0000 90.0000 120.0000 >> >> * Resolution Range : >> >> 0.00043 0.11138 ( 48.225 - 2.996 A ) >> >> * Sort Order : >> >> 1 2 3 0 0 >> >> * Space group = 'P 3 2 1' (number 150) >> >> >> >> OVERALL FILE STATISTICS for resolution range 0.000 - 0.111 >> ======================= >> >> >> Col Sort Min Max Num % Mean Mean Resolution >> Type Column num order Missing complete abs. >> Low High label >> >> 1 ASC 0 29 0 100.00 13.7 13.7 48.22 3.00 >> H H 2 NONE 0 16 0 100.00 4.7 4.7 48.22 >> 3.00 H K 3 NONE -32 32 0 100.00 0.5 12.2 >> 48.22 3.00 H L 4 NONE 1.4 291.9 0 100.00 19.40 >> 19.40 48.22 3.00 F FP 5 NONE 0.1 4.3 0 100.00 >> 0.67 0.67 48.22 3.00 Q SIGFP 6 NONE -13.6 13.2 69 >> 99.41 -0.01 0.69 48.22 3.00 D DANO 7 NONE 0.0 >> 5.7 69 99.41 1.13 1.13 48.22 3.00 Q SIGDANO 8 >> NONE 0 2 0 100.00 0.0 0.0 48.22 3.00 >> Y ISYM 9 NONE 0.0 1.0 0 100.00 0.95 0.95 >> 48.22 3.00 I FreeRflag >> >> >> No. of reflections used in FILE STATISTICS 11643 >> >> >> Aren't they supposed to be the exact same number? >> >> Thanks, ciao, s >> >> >> On Jan 16, 2013, at 1:12 PM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> >> wrote: >> >> Dear Sebastiano, >> >> you could use xprep to get the statistics in user defined >> resolution shells. >> >> Out of curiosity: Would you mind sharing why you want to do this >> and why you don't want to use the XSCALE statistics instead? The >> statistics are probably more meaningful after scaling, I guess. >> >> Best, Tim >> >> On 01/15/2013 04:22 PM, Sebastiano Pasqualato wrote: >>>>> >>>>> Hi all, I was wondering if XDS allows to change the number >>>>> of resolution bins appearing in the table: >>>>> >>>>> SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS >>>>> FUNCTION OF RESOLUTION >>>>> >>>>> of CORRECT.LP. >>>>> >>>>> Please, note that I am not referring to the table output by >>>>> XSCALE, in which you can change the resolution bins with the >>>>> keyword RESOLUTION_SHELLS=, but rather the table output by >>>>> the CORRECT job of XDS. >>>>> >>>>> Thanks in advance, ciao, Sebastiano >>>>> >>>>> >> >> >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFQ9qj9UxlJ7aRr7hoRAic9AJ9P8Yg7qoSwtKETrt1uVV9zmzrddgCgz3Ub > Gd+HUldC4e4RDI7f7qzJtTw= > =xABX > -----END PGP SIGNATURE----- -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
