2VB1: Difference between revisions

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ORGX=3130 ORGY=3040 ! for ADSC, header values are subject to interpretation; these values from visual inspection

! the following is for masking the beamstop shadow in sweeps c-d

UNTRUSTED_RECTANGLE==0 3189 2960 3087 ! use XDS-viewer of ADXV to find the values

UNTRUSTED_RECTANGLE=0 3189 2960 3087 ! use XDS-viewer of ADXV to find the values

! the following is for sweeps e-h

UNTRUSTED_RECTANGLE=1 3160 3000 3070

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8.182E+00 1.759E-04 26.36 27.60 ../g/XDS_ASCII.HKL

7.717E+00 3.694E-04 18.73 21.93 ../h/XDS_ASCII.HKL

and there are about 1500 rejected reflections.

and there are about 1500 rejected reflections. It is reassuring to note that the error model works well; the ISa goes down toward sweep h probably because the crystal degrades. But see also the "a posterior remarks" below - sweep h is the one that is most affected by a shadow on the detector.

SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION

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So there is still useful signal beyond 0.65 A.

~~Remark:~~ The first frames of sweeps g and h show a shadow in one corner of the detector. Nothing was done by me to exclude this shadow from processing (but one should do so if the resolution should be expanded beyond 0.65 A which the XSCALE statistics suggest to be possible). ~~There~~ is ~~however~~ no facility in XDS to exclude bad areas of specific frames in a dataset; one ~~would need~~ to chop the dataset into ~~two~~ parts.

== Some ''a posteriori'' remarks ==

* For sweeps e-h one should use TRUSTED_REGION= 0 1.2 since that already gives 0.626 A in the corners.

* The first and last frames of sweeps g and h show a shadow in one corner of the detector. Nothing was done by me to exclude this shadow from processing (but one should do so at least if the resolution should be expanded beyond 0.65 A which the XSCALE statistics suggest to be possible). <br> One could experiment with MINIMUM_VALID_PIXEL_VALUE= 40 (or so) instead of 1 - I'd probably try that, but of course one does not want to exclude valid pixels so the result has to be carefully checked. <br> Anyway, there is no general facility in XDS to exclude bad areas of ''specific'' frames in a dataset; one needs to chop the dataset into parts and deal with each shadow separately.

== Comparison of data processing: published (2006) ''vs'' XDS results ==

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</table>

== ~~Data~~ from XDS processing ==

== Availability of data from XDS processing ==

I changed XSCALE.INP to have

!FRIEDEL'S_LAW=TRUE ! by commenting it out XSCALE will use FRIEDEL'S_LAW=FALSE

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Line 357:

EOF

and obtain output_file_name.mtz which I mv to [~~ftp~~://~~turn5.biologie.uni-konstanz.de~~/pub/xds-datared/2vb1/xds-hewl-I.mtz xds-hewl-I.mtz]. SFCHECK statistics for this file are [~~ftp~~://~~turn5.biologie.uni-konstanz.de~~/pub/xds-datared/2vb1/sfcheck_XXXX.pdf here].

and obtain output_file_name.mtz which I mv to [https://{{SERVERNAME}}/pub/xds-datared/2vb1/xds-hewl-I.mtz xds-hewl-I.mtz]. SFCHECK statistics for this file are [https://{{SERVERNAME}}/pub/xds-datared/2vb1/sfcheck_XXXX.pdf here].

Similarly, using OUTPUT_FILE=temp.hkl CCP4 I obtained a file with amplitudes, [~~ftp~~://~~turn5.biologie.uni-konstanz.de~~/pub/xds-datared/2vb1/xds-hewl-F.mtz xds-hewl-F.mtz]

Similarly, using OUTPUT_FILE=temp.hkl CCP4 I obtained a file with amplitudes, [https://{{SERVERNAME}}/pub/xds-datared/2vb1/xds-hewl-F.mtz xds-hewl-F.mtz]

@@ Line 7: / Line 7: @@
   ORGX=3130 ORGY=3040  ! for ADSC, header values are subject to interpretation; these values from visual inspection
   ! the following is for masking the beamstop shadow in sweeps c-d
-  UNTRUSTED_RECTANGLE==0 3189 2960 3087 ! use XDS-viewer of ADXV to find the values
+  UNTRUSTED_RECTANGLE=0 3189 2960 3087 ! use XDS-viewer of ADXV to find the values
   ! the following is for sweeps e-h
   UNTRUSTED_RECTANGLE=1 3160 3000 3070
@@ Line 260: / Line 260: @@
 .182E+00  1.759E-04   26.36   27.60 ../g/XDS_ASCII.HKL
 .717E+00  3.694E-04   18.73   21.93 ../h/XDS_ASCII.HKL
-and there are about 1500 rejected reflections.
+and there are about 1500 rejected reflections. It is reassuring to note that the error model works well; the ISa goes down toward sweep h probably because the crystal degrades. But see also the "a posterior remarks" below - sweep h is the one that is most affected by a shadow on the detector.
   SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
@@ Line 293: / Line 293: @@
 So there is still useful signal beyond 0.65 A.
-Remark: The first frames of sweeps g and h show a shadow in one corner of the detector. Nothing was done by me to exclude this shadow from processing (but one should do so if the resolution should be expanded beyond 0.65 A which the XSCALE statistics suggest to be possible). There is however no facility in XDS to exclude bad areas of specific frames in a dataset; one would need to chop the dataset into two parts.
+== Some ''a posteriori'' remarks ==
+* For sweeps e-h one should use TRUSTED_REGION= 0 1.2 since that already gives 0.626 A in the corners.
+* The first and last frames of sweeps g and h show a shadow in one corner of the detector. Nothing was done by me to exclude this shadow from processing (but one should do so at least if the resolution should be expanded beyond 0.65 A which the XSCALE statistics suggest to be possible). <br> One could experiment with MINIMUM_VALID_PIXEL_VALUE= 40 (or so) instead of 1 - I'd probably try that, but of course one does not want to exclude valid pixels so the result has to be carefully checked. <br> Anyway, there is no general facility in XDS to exclude bad areas of ''specific'' frames in a dataset; one needs to chop the dataset into parts and deal with each shadow separately.
 == Comparison of data processing: published (2006) ''vs'' XDS results ==
@@ Line 334: / Line 338: @@
 </table>
-== Data from XDS processing ==
+== Availability of data from XDS processing ==
 I changed XSCALE.INP to have
   !FRIEDEL'S_LAW=TRUE  ! by commenting it out XSCALE will use FRIEDEL'S_LAW=FALSE
@@ Line 353: / Line 357: @@
   EOF
-and obtain output_file_name.mtz which I mv to [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2vb1/xds-hewl-I.mtz xds-hewl-I.mtz]. SFCHECK statistics for this file are [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2vb1/sfcheck_XXXX.pdf here].
+and obtain output_file_name.mtz which I mv to [https://{{SERVERNAME}}/pub/xds-datared/2vb1/xds-hewl-I.mtz xds-hewl-I.mtz]. SFCHECK statistics for this file are [https://{{SERVERNAME}}/pub/xds-datared/2vb1/sfcheck_XXXX.pdf here].
-Similarly, using OUTPUT_FILE=temp.hkl CCP4 I obtained a file with amplitudes, [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2vb1/xds-hewl-F.mtz xds-hewl-F.mtz]
+Similarly, using OUTPUT_FILE=temp.hkl CCP4 I obtained a file with amplitudes, [https://{{SERVERNAME}}/pub/xds-datared/2vb1/xds-hewl-F.mtz xds-hewl-F.mtz]