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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 <[log in to unmask]>
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
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