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Wishlist: Difference between revisions
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== Bugs == | == Bugs == | ||
* FRAME.cbf does not have distance and wavelength information, as well as direct beam position - would be good to have those for adxv usage. | * FRAME.cbf does not have distance and wavelength information, as well as direct beam position - would be good to have those for adxv usage. | ||
* When scaling multiple datasets with multiple OUTPUT entries within the same XSCALE.INP file, the reported statistics within XSCALE.LP does respect the corresponding INCLUDE_RESOLUTION_RANGE= keyword entries. --[[User:Mnfodje|Mnfodje]] June 24, 2011 <br> ''Comment: XSCALE finds the highest high-resolution cutoff of all output datasets, and prints out statistics for all datasets up to this resolution. Depending on the user-input values of INCLUDE_RESOLUTION_RANGE= , this may lead to tables that e.g. have 0 reflections in the high-resolution bin(s). This does not affect the data that are output; the only number (I think) that is wrong in those tables is the value for the total completeness. The workaround to get that value obviously is running XSCALE separately for each resolution-truncated dataset. --[[User:Kay|Kay]] 18:21, 25 June 2011 (CEST)'' | * When scaling multiple datasets with multiple OUTPUT entries within the same XSCALE.INP file, the reported statistics within XSCALE.LP does respect the corresponding INCLUDE_RESOLUTION_RANGE= keyword entries. --[[User:Mnfodje|Mnfodje]] June 24, 2011 <br> ''Comment: XSCALE finds the highest high-resolution cutoff of all output datasets, and prints out statistics for all datasets up to this resolution. Depending on the user-input values of INCLUDE_RESOLUTION_RANGE= , this may lead to tables that e.g. have 0 reflections in the high-resolution bin(s). This does not affect the data that are output; the only number (I think) that is wrong in those tables is the value for the total completeness. The workaround to get that value obviously is running XSCALE separately for each resolution-truncated dataset. --[[User:Kay|Kay]] 18:21, 25 June 2011 (CEST)'' | ||
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== Would be nice to have == | == Would be nice to have == | ||
* Add the REIDX keyword to XDSCONV. This would enable scaling in a centered spacegroup, and using P1 for the final dataset. | * Add the REIDX keyword to XDSCONV. This would enable scaling in a centered spacegroup, and using P1 for the final dataset. | ||
* Add a SKIP_RANGE keyword similar to SPOT_RANGE which enables skipping multiple ranges of frames from the specified DATA_RANGE. XDS should just ignore those frames as if they were supposed to exist but do not. --[[User:Mnfodje|Mnfodje]] 15:07, 1 November 2010 (UTC). ''Comment: | * Add a SKIP_RANGE keyword similar to SPOT_RANGE which enables skipping multiple ranges of frames from the specified DATA_RANGE. XDS should just ignore those frames as if they were supposed to exist but do not. --[[User:Mnfodje|Mnfodje]] 15:07, 1 November 2010 (UTC). ''Comment: there is EXCLUDE_DATA_RANGE for this purpose'' | ||
* if the first frame of DATA_RANGE cannot be found in CORRECT (because the frames have already been deleted or so), xds should pick up QX, QY, NX, NY from XDS.INP. ''Fixed in the version of Dec 06, 2010'' | * if the first frame of DATA_RANGE cannot be found in CORRECT (because the frames have already been deleted or so), xds should pick up QX, QY, NX, NY from XDS.INP. ''Fixed in the version of Dec 06, 2010'' | ||
* A breakdown of R<sub>meas</sub> by frame number, as currently only available from [[XDSSTAT]]. | * A breakdown of R<sub>meas</sub> by frame number, as currently only available from [[XDSSTAT]]. | ||
* Templates of XDS.INP currently have | * Templates of XDS.INP currently have | ||
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* a keyword REJECT_ALIEN= with a default of 20. This would be the cutoff for automatic rejection of "aliens". See [[Optimization#Wilson%20outliers%20(aliens)]]--[[User:Kay|Kay]] 10:29, 27 November 2007 (CET). '' This was implemented in January 2010.'' | * a keyword REJECT_ALIEN= with a default of 20. This would be the cutoff for automatic rejection of "aliens". See [[Optimization#Wilson%20outliers%20(aliens)]]--[[User:Kay|Kay]] 10:29, 27 November 2007 (CET). '' This was implemented in January 2010.'' | ||
* Automated Direct Beam Position Recognition from Direct Beam Shots: The [[Features that are not officially documented|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.--[[User:Tmaier|Tmaier]] 13:24, 13 December 2007 (CET) | * Automated Direct Beam Position Recognition from Direct Beam Shots: The [[Features that are not officially documented|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.--[[User:Tmaier|Tmaier]] 13:24, 13 December 2007 (CET) | ||
* Option to write out FRAME.PCK for visual control | * Option to write out FRAME.PCK for visual control of specific images: this is available from the "tools" tab of XDSGUI. | ||
* 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. | * 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. | ||
* In CORRECT.LP, there is a section "SUMMARY OF DATA SET STATISTICS FOR VARIOUS SUBSETS OF INCLUDED DATA IMAGES", which outputs data set statistics for a subset of the image with an image increment. They are very useful to determine where I should stop for processing. For example, if I found that the Rmeas and I/sigma of image 1-180 are worse than those of image 1-160. I then will only process image 1-160, because the last 20 images doesn't add more signal to my data. However, the image increment is automatically determined by CORRECT, which is a rather large number. It would be nice to have an option to set the image increment by users to help determine when the crystal dies. --[[User:Jzhu|Jzhu]] 04:53, 27 June 2011 (CEST) ''Comment: CORRECT prints statistics for 9 pieces of the DATA_RANGE. In the absence of an option to modify that number, the workaround is probably to run XDSSTAT to get Rmeas and I/sigma of the individual frames.'' --[[User:Kay|Kay]] 11:08, 2 April 2012 (CEST) | * In CORRECT.LP, there is a section "SUMMARY OF DATA SET STATISTICS FOR VARIOUS SUBSETS OF INCLUDED DATA IMAGES", which outputs data set statistics for a subset of the image with an image increment. They are very useful to determine where I should stop for processing. For example, if I found that the Rmeas and I/sigma of image 1-180 are worse than those of image 1-160. I then will only process image 1-160, because the last 20 images doesn't add more signal to my data. However, the image increment is automatically determined by CORRECT, which is a rather large number. It would be nice to have an option to set the image increment by users to help determine when the crystal dies. --[[User:Jzhu|Jzhu]] 04:53, 27 June 2011 (CEST) ''Comment: CORRECT prints statistics for 9 pieces of the DATA_RANGE. In the absence of an option to modify that number, the workaround is probably to run XDSSTAT to get Rmeas and I/sigma of the individual frames.'' --[[User:Kay|Kay]] 11:08, 2 April 2012 (CEST) | ||