Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP
Dear Sebastiano, sorry, it is not possible. Indeed, only XCSALE allows you to define the resolution ranges yourself. HTH, Kay On Tue, 15 Jan 2013 16:22:14 +0100, Sebastiano Pasqualato sebastiano.pasqual...@gmail.com 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
Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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/ iD8DBQFQ9pk/UxlJ7aRr7hoRAqreAJ9/aKSHyXWahBc96/3x0U5iriZk4gCg2fWC GVLgXUEN+10M9IpCDRENGF0= =SK0P -END PGP SIGNATURE-
Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP
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 : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 292.0 0 100.0019.4019.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.70 0.70 48.22 3.00 Q SIGFP 6 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11551 =FALSE: 11643 reflections * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 100.5450 100.5450 96.4500 90. 90. 120. * Resolution Range : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 291.9 0 100.0019.4019.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.67 0.67 48.22 3.00 Q SIGFP 6 NONE -13.613.269 99.41-0.01 0.69 48.22 3.00 D DANO 7 NONE0.0 5.769 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 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11643 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: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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/ iD8DBQFQ9pk/UxlJ7aRr7hoRAqreAJ9/aKSHyXWahBc96/3x0U5iriZk4gCg2fWC GVLgXUEN+10M9IpCDRENGF0= =SK0P -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
Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP
-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. 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. 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 : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 292.0 0 100.0019.40 19.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.70 0.70 48.22 3.00 Q SIGFP 6 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11551 =FALSE: 11643 reflections * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 100.5450 100.5450 96.4500 90. 90. 120. * Resolution Range : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 291.9 0 100.0019.40 19.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.67 0.67 48.22 3.00 Q SIGFP 6 NONE -13.613.269 99.41-0.01 0.69 48.22 3.00 D DANO 7 NONE0.0 5.769 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 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11643 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/
Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP
The XDS CORRECT step will also (by default) do scaling - if I understand correctly the same scaling as in XSCALE, but for a single sweep and with no zero-dose. If what you want is merging statistics, I find it helpful to write out the data unmerged and then use pointless -c and aimless to merge the data (with scales constant) which provides a very nice summary. Best wishes, Graeme On 16 January 2013 13:19, 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. 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. 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 : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 292.0 0 100.0019.40 19.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.70 0.70 48.22 3.00 Q SIGFP 6 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11551 =FALSE: 11643 reflections * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 100.5450 100.5450 96.4500 90. 90. 120. * Resolution Range : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 291.9 0 100.0019.40 19.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.67 0.67 48.22 3.00 Q SIGFP 6 NONE -13.613.269 99.41-0.01 0.69 48.22 3.00 D DANO 7 NONE0.0 5.769 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 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11643 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
Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP
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 : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 292.0 0 100.0019.40 19.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.70 0.70 48.22 3.00 Q SIGFP 6 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11551 =FALSE: 11643 reflections * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 100.5450 100.5450 96.4500 90. 90. 120. * Resolution Range : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 291.9 0 100.0019.40 19.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.67 0.67 48.22 3.00 Q SIGFP 6 NONE -13.613.269 99.41-0.01 0.69 48.22 3.00 D DANO 7 NONE0.0 5.769 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 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11643 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
Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP
Sebastiano, CORRECT does scale the data. XSCALE is only needed for two or more datasets, or if other requirements exist - you named one. The two varieties of FRIEDEL'S_LAW differ in their rejections! HTH, Kay Sebastiano Pasqualato sebastiano.pasqual...@gmail.com schrieb: 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 : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 292.0 0 100.0019.4019.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.70 0.70 48.22 3.00 Q SIGFP 6 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11551 =FALSE: 11643 reflections * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 100.5450 100.5450 96.4500 90. 90. 120. * Resolution Range : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 291.9 0 100.0019.4019.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.67 0.67 48.22 3.00 Q SIGFP 6 NONE -13.613.269 99.41-0.01 0.69 48.22 3.00 D DANO 7 NONE0.0 5.769 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 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11643 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: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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/ iD8DBQFQ9pk/UxlJ7aRr7hoRAqreAJ9/aKSHyXWahBc96/3x0U5iriZk4gCg2fWC GVLgXUEN+10M9IpCDRENGF0= =SK0P -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
Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP
Excellent. Thanks a lot for the clarifications. ciao, s On Jan 16, 2013, at 4:14 PM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: Sebastiano, CORRECT does scale the data. XSCALE is only needed for two or more datasets, or if other requirements exist - you named one. The two varieties of FRIEDEL'S_LAW differ in their rejections! HTH, Kay Sebastiano Pasqualato sebastiano.pasqual...@gmail.com schrieb: 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 : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 292.0 0 100.0019.4019.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.70 0.70 48.22 3.00 Q SIGFP 6 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11551 =FALSE: 11643 reflections * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 100.5450 100.5450 96.4500 90. 90. 120. * Resolution Range : 0.000430.11138 ( 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 SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh 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 NONE1.4 291.9 0 100.0019.4019.40 48.22 3.00 F FP 5 NONE0.1 4.3 0 100.00 0.67 0.67 48.22 3.00 Q SIGFP 6 NONE -13.613.269 99.41-0.01 0.69 48.22 3.00 D DANO 7 NONE0.0 5.769 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 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11643 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: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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 -
[ccp4bb] changing resolution bins statistics in CORRECT.LP
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 -- 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 sebastiano.pasqual...@ieo.eu
