Difference between revisions of "Wishlist"

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* Option to write out FRAME.PCK for visual control for every nth image, e.g. controlled by a keyword "FRAMEPCK_EVERY_NTH=" with default FRAMEPCK_EVERY_NTH=0 i.e. single FRAME_NTH.PCK as in current version, the option  FRAMEPCK_EVERY_NTH=B i.e. writing one FRAME_NTH.PCK per batch in INTEGRATE, and the option to provide an integer number n to get FRAME_NTH.PCK for every nth original image.--[[User:Tmaier|Tmaier]] 13:37, 13 December 2007 (CET)
 
* Option to write out FRAME.PCK for visual control for every nth image, e.g. controlled by a keyword "FRAMEPCK_EVERY_NTH=" with default FRAMEPCK_EVERY_NTH=0 i.e. single FRAME_NTH.PCK as in current version, the option  FRAMEPCK_EVERY_NTH=B i.e. writing one FRAME_NTH.PCK per batch in INTEGRATE, and the option to provide an integer number n to get FRAME_NTH.PCK for every nth original image.--[[User:Tmaier|Tmaier]] 13:37, 13 December 2007 (CET)
  
* Option to produce harvest files from CORRECT and XSCALE for deposition of structures.--[[User:Graeme||Graeme]] 18 February 2008.
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* Option to produce harvest files from CORRECT and XSCALE for deposition of structures.--[[User:Graeme|Graeme]] 18 February 2008. Clarifying this in response to question: Mosflm and Scala both produce files which contain information which can be included at deposition - this is produced as separate Harvest files, based on the statistics already generated by the programs. These harvest files are in mmCIF format, and I will upload a couple if I can figure out how. This does require a certain amount of administrative information (a "name" for the project and dataset) but could be easily rectified by adding a keyword: HARVEST_PROJECT= HARVEST_DATASET= which could then produce PROJECT_DATASET.xds or .xscale depending on the program. [[User:Graeme|Graeme]] 30 May 2008.
  
 
== Cosmetical ==
 
== Cosmetical ==

Revision as of 14:11, 30 May 2008

This is a collection of things users feel XDS should handle differently from how the program currently does.

On this page (only), it would seem useful if a user who edits this puts his "signature with timestamp" (second button from the right in the edit menu bar) after the sentence s/he inserts.


Important

  • CORRECT should print out the parameter of STRICT_ABSORPTION_CORRECTION= . The influence of this on the anomalous signal is significant, and it is difficult to compare data reductions without its value being documented in CORRECT.LP . --Kay 23:30, 22 December 2007 (CET)

Would be nice to have

  • IDXREF should print out the maximum oscillation angle for a mosaicity of zero, according to delta-φmax=(longest primitive cell axis)/dmax*180°/Pi where dmax is at the edge of the detector. This could be printed near the bottom of the file, after the second "aP" line (which has the P1 cell).--Kay 10:43, 13 May 2008 (CEST)
  • A breakdown of Rmeas by frame number, as currently only available from XDSSTAT. This would be useful in order to identify bad frames. --Kay 14:00, 12 November 2007 (CET)
  • Templates of XDS.INP currently have
!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 3.47 3.41 !ice-ring at 3.441 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.70 2.64 !ice-ring at 2.671 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.28 2.22 !ice-ring at 2.249 Angstrom

This list may/could be completed by

!EXCLUDE_RESOLUTION_RANGE= 2.102 2.042 !ice-ring at 2.072 Angstrom - should be strong
!EXCLUDE_RESOLUTION_RANGE= 1.978 1.918 !ice-ring at 1.948 Angstrom - may be weak
!EXCLUDE_RESOLUTION_RANGE= 1.948 1.888 !ice-ring at 1.918 Angstrom - should be strong
!EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - may be weak
!EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - may be weak

Please note that I did not optimize the widths (in particular the last one should probably be something like 1.741 1.701 or 1.731 1.711), and that the ranges of the 2nd, 3rd and 4th ring overlap (and thus could be combined and narrowed to something like 1.958 1.873). --Kay 14:30, 12 November 2007 (CET)

  • INCLUDE_RESOLUTION_RANGE= should be respected by IDXREF because this could be used to prevent ice rings from disturbing the indexing. Drawback: one would have to change INCLUDE_RESOLUTION_RANGE= after running IDXREF.
    Probably better: EXCLUDE_RESOLUTION_RANGE= should be respected by IDXREF. Drawback: geometrical parameters (in particular the direct beam position) are unrefined when resolution is calculated in IDXREF.
    Probably best: a new keyword for this purpose.
    For a workaround, see Ice_rings.
    Based on discussion with Clemens Vonrhein --Kay 12:16, 16 November 2007 (CET)
  • an error message and program stop if the files given as parameters of X-GEO_CORR and Y-GEO_CORR cannot be found. Currently the program continues silently, which might lead to suboptimally processed data.--Kay 22:19, 12 December 2007 (CET)
  • Automated Direct Beam Position Recognition from Direct Beam Shots: The undocumented DIRB option should be announced and extended. I would suggest the following: a new input keyword "NAME_OF_DIRB_FRAME=" instead of interactive input is used to specifiy the direct beam shot frame. As a default "NAME_OF_DIRB_FRAME=" should use frame 0 of the current Name_Template_of_data_frames selection. Avoiding interactive input would facilitate automated script based processing and avoid the use of erroneous direct beam position from headers or manual input.--Tmaier 13:24, 13 December 2007 (CET)
  • Option to write out FRAME.PCK for visual control for every nth image, e.g. controlled by a keyword "FRAMEPCK_EVERY_NTH=" with default FRAMEPCK_EVERY_NTH=0 i.e. single FRAME_NTH.PCK as in current version, the option FRAMEPCK_EVERY_NTH=B i.e. writing one FRAME_NTH.PCK per batch in INTEGRATE, and the option to provide an integer number n to get FRAME_NTH.PCK for every nth original image.--Tmaier 13:37, 13 December 2007 (CET)
  • Option to produce harvest files from CORRECT and XSCALE for deposition of structures.--Graeme 18 February 2008. Clarifying this in response to question: Mosflm and Scala both produce files which contain information which can be included at deposition - this is produced as separate Harvest files, based on the statistics already generated by the programs. These harvest files are in mmCIF format, and I will upload a couple if I can figure out how. This does require a certain amount of administrative information (a "name" for the project and dataset) but could be easily rectified by adding a keyword: HARVEST_PROJECT= HARVEST_DATASET= which could then produce PROJECT_DATASET.xds or .xscale depending on the program. Graeme 30 May 2008.

Cosmetical

  • CORRECT should print out MAXIMUM_NUMBER_OF_PROCESSORS= , and the actual number of processors used. --Kay 13:55, 12 November 2007 (CET)
  • CORRECT should print out MINIMUM_I/SIGMA= . --Kay 14:24, 13 November 2007 (CET)
  • BACKGROUND_RANGE= should have a better default (e.g., the first five frames of the DATA_RANGE). The default currently appears to be 0 0. --Kay 14:45, 12 November 2007 (CET)
  • document X-GEO_CORR and Y-GEO_CORR.--Kay 22:18, 12 December 2007 (CET)