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What's new in CrystalClear™ 1.3.6 SP2 

There are a few new features in CrystalClear 1.3.6SP2, as well as many bug fixes and enhancements.

New Features

The new features that are available in CrystalClear 1.3.6SP2 are:

• Implementation of "Small Molecule" mode for data collection and processing.
• Support for AFC12/Kappa goniometer and SPIDER imaging plate system.
• Implemented Collision detection methodology using supporting XML files to determine valid rotation axis ranges to avoid collisions with detectors, etc.
• Incorporated support for new batch restraint capability in dtscaleaverage.

Bug fixes/Enhancements

The bug fixes/enhancements that are available in CrystalClear 1.3.6SP2 are:

• Enhancements
  • Updated small molecule CrystalClear instrument site default files for RAPID, Spider, AFC7, AFC8,AFC10, and AFC12 (Saturn and Mercury) instruments.
  • Modified InstallShield installation to ensure new HTML file group help files always get installed during a Repair upgrade.
  • Added logging of instrument configuration file options.
  • Reorganized the dtstrategy summary output. Now it shows a single scan summary AND the best multiple scan solution, if available.
  • Enhanced warning message which displays indicating substantially large detector goniometer refinement changes and prompting user which scans to allow application of such large changes. The enhancement involves displaying on the message box a list of which detector goniometer values met one of two possible criteria for being designated as "substantially large changes".
  • Added message that warns and prompts user whether to change instrument type in Administrator Utilities dialog.
  • Added image viewer utility to change image viewer text font and text size.
  • Added message to warn user to reset crystal system and lattice type after doing a manual transform in the Transform Cell dialog.
  • Added utility to select one or more ice ring resolutions as custom resolution arcs in the Set Resolution dialog associated with the image viewer.
  • Placement of file creation time stamp and CrystalClear version at beginning of all d*TREK generated log files.
  • Enabled selection of application type (macromolecular or small molecule) from InstallShield install setup. Also added menu items to allow dynamic changing of application type.
  • Improved certain CIF output. This includes ensuring Z-value gets written from first the numerical absorption correction processing. If numabs.log is not available, then determine Z-value from the molecular formula if specified. If molecular formula not specified, then get a default Z-value based on current cell Laue class.
  • Improved reporting of missing mask files on a per scan basis.
  • Attenuator GUI now passes number of cycles to instrument server.
  • Dark current now subtracted when taking direct beam shots on CCDs.
  • Improvements to remaining collection time estimates (initial estimates may be wildly off due to small sampling size).
  • Added support for StopAfterImage feature, and -log command line option for specifying log file directory in instrument servers.
  • Added support for new log file versioning nomenclature
• Bug fixes: CrystalClear
  • Fixed problem in d*TREK Strategy advanced tab dialog where maximum rotation range may be set as zero if not found in strategy dialog database, resulting from defaults not containing this parameter.
  • Fixed problem in Windows XP installation when updating unsigned Marx dongle drivers caused by interfering Windows warning message. Updated CBSetup.exe which now installs signed drivers avoiding warning message. Also changed InstallShield installation to install dongle drivers before displaying InstallShield finish dialog.
  • Fixed problem with parameters not being stored between CrystalClear sessions in Tools->Administration->Servers tab.
  • Fixed About box graphic for CrystalClear-SM to represent the small molecule graphic
  • Fixed CrystalClear to properly handle strategy when running a Process-only task. This utility was enhanced to extract crystal and detector goniometer rotation range extents from a process-only sample's image header if available, and if not available to prompt the user for such values. Strategy results are displayed in the dtstrategy.log file.
  • Fixed problem with CrystalClear hanging because of socket congestion when navigating collection dialog scan tables because of too many many schedule scans and/or rapid navigation through table fields possible when using the keyboard.
  • Fixed CrystalClear hanging whenever screen images only are collected in a Collect and Process task.
  • Fixed problem when running small molecule CrystalClear where an erroneous Find Matrix Results dialog is displayed when the Reduce Cell flow bar button is clicked after transforming the current cell using the Cell Transformation utility from the Processing->Cell Tools menu.
  • Fixed problem with the Take Axial Photo dialog no longer reporting any configurations (available or unavailable) for combination axial directions (a+b, a+c, b+c, a+b+c, 2a+b).
  • Fixed a maximum rotation range problem in dtstrategy where entering a rangemax which isless than the available maximum range but more than what is expected to give the desired completeness always produced scans whose range equals the specified rangemax value.
  • Fixed problem with the dynamic mask for the RAPID not properly being interpreted when the 200x200 micron pixel size is used to collect data.
  • Fixed problem with StopInstrument.exe process task not being terminated in the Windows environment when switching from collection task to a process-only task in CrystalClear.
  • Fixed problems assocauted with assigning spacegroup number during CrystalClear processing steps based only using crystal system, Laue class, and centricity as spacegroup number narrowing parameters. Fixed CrystalClear to also use lattice type as a defining parameter. Problems were observed during the Laue check operation when non-primitive lattice type cells were being assigned spacegroup numbers for primitive cells. Fix also includded adding a Lattice type combo box to the Processing State Display and Setup->Crystal2 dialogs where full spacegroup information is displayed.
  • Fixed problem with CrystalClear crashing when Escape key is pressed under specific circumstances when in the simple mask file specification of the Setup->Detector->Advanced dialog.
  • Fixed problem for d*TREK processing steps not placing a -reso command option if user set the min and max resolution values to be the same (and non-zero). Now, the -reso will only not be placed for one special case: if both min and max are identically zero. Also added messagebox prompt to user whether he wants to continue processing if he does enter the same min and max non-zero resolution values.
  • Fixed problem with long delay in display of the input dialog for the image viewer Min, Max, Average, and Tile Images functions caused by counting the number of availble collected images. Operations fixed to only count up to the first 10 images, not all images.
  • Implemented detector distance and 2-theta validation checks against instrument server configured valid ranges. Warning messages display if user attempts to collect an out of range value for either parameter. Also added a display of the current instrument server provided ranges for the convenience of the user on the "Double-Check Settings" dialog that pops-up on non-RAPID/SPIDER instruments when the Run button is clicked in the collect images dialogs.
  • Fixed problem with Index Results dialog not selecting the same default orientation angles solution as the default determined by dtindex. The default solution is now highlighted when the Index Results dialog is displayed.
  • Fixed problem with output image of an Expose and Read operation in the CCD Manual Instrument Control not being properly written to disk with a known filename. Fix involved adding a user-specifiable filename edit field within the Expose and Read groupbox and ensuring instrument server writes the output image to this filename.
  • Fixed problem with not being able to tab past the rotation axis column (if displayed) in the scan table of either the image collection dialogs or the Scan State Display dialog.
  • Fixed problem with JDTPlot not always displaying all of the plots on the main page (summary page) of the plots.
  • Removed display of the "Double-Check Settings" warning message dialog (which appears after clicking Run in the image collection dialogs) for RAPID/SPIDER instruments since distance is fixed and 2-theta is undefined. Fixed problem with the advanced tab in the strategy dialog allowing editing of the distance field for the RAPID/SPIDER instruments. Field is now read-only.
  • Fixed problem with CrystalClear not informing collection instrument server the location of the sample image directory when switching back to a collection task from a process-only task without closing sample.
  • Fixed problem with number of shots value for direct beam shots in Administrator Utiliities dialog not being sent to CCD instrument server.
  • Fixed problem in CIF writing utility in small molecule CrystalClear where certain fields whose information is normally extracted from dtrefine.log (which is not written in small molecule CrystalClear). Information is now extracted from the specific refine files that CrystalClear-SM does write.
  • Fixed problem where default "batch restraint" was not properly handled by dtscaleaverage.
  • Removed 10 image maximum restriction for pre-find + refine before integration processing.
  • Fixed problem in TwinSolve where the crystal having ID = 1 was being inadverently deleted and reconstructed from the default crystal if no twin information had not yet calculated.
  • Fixed problem with Reduce Cell button not working on the d*TREK Reduce Cell dialog in small molecule CrystalClear processing.
  • Fixed problem resulting from use of "FirstScanImage" keyword for simple masks (necessary for d*TREK processing) when using TwinSolve. Now, when TwinSolve is used, the mask file entry is blanked out, preventing TwinSolve from thinking FirstScanImage is an actual file.
  • Fixed problem with Instrument State Display, Scan State Display, Processing State Display, and Manual Instrument Control dialogs not restoring to normal size after having been previously minimized when user clicks corresponding toolbar button.
  • Fixed cropping problem with initial display size of Scan State Display. Before, the dialog was displayed so that the full scan table was not displayed and user would have to manually resize formview window to see whole scan table.
  • Fixed problem where confusing information messagebox appears resulting from site default file having an ?Unknown? molecule type after an installation upgrade. Fixed so that if this value is set at ?Unknown?, value gets automatically updated to be that found in application.configuration file.
  • Fixed problem with default collect scan distance getting reset to zero when running a recipe from Director.
• Bug fixes: Instrument servers
  • Omega axis motor start speed adjusted to be 50 deg/minute for AFC10, AFC11 and AFC12. (CCD)
  • Added configuration file option (in MSCServDetCCD.configuration) for indicating that the phi axis should be datumed before starting data collection. Option is: DatumPhiBeforeCollection = On | Off (Off is default) (CCD)
  • Added check to see if scan speed is allowed before starting data collection. (CCD)
  • Removed inclusion of trigger delays in exposure time used in the ExposeAndRead command. (CCD)
  • Both IP plate positions are updated in configuration file for R-AXIS II (even though only the one for IP#1 is used).
  • Added support for taking still images. (R-AXIS)
  • Fixed bug in which shutter state would indicate open, but elapsed time would be 0, when exposure time was less than readout time. (RAXIS)
  • Fixed problem of instrument server mislabeling overload correction images as dezingered images and displaying as such in the Instrument State Display. (CCD)
  • Fixed instrument server communication problems causing CrystalClear to sometimes hang by eliminating unnecessary GetImageSize queries to the instrument detector. Now such queries are only done at instrument startup. (CCD)
  • Support for attenuators for the AFC8. (CCD)
  • Added capability for R-AXIS II to do multiple direct beam shots, if specified. (RAXIS)
  • Fixed problem with current date and time not being updated in the image headers. (CCD) Fixed bug in setting saturated value for pixel in images when overload correction used. (CCD)
• Bug fixes: d*TREK
  • Improved cumulative intensity distributions plots by fixing the d*TREK dtintegrate module as follows:
    • If -noprofit dtintegrate option is used, then a dtprofit.ref file is still created, but the intensities in that file have no contribution from profile-fitting. However, some other things such as trimming away noisy tails is done with the non-profile-fitted intensities.
    • If -profit dtintegrate option is used, the number of reflections that are not profile-fitted is reduced.
  • Fixed crash in d*TREK absorption correction module when -fourier option is selected.
  • Fixed math problem in d*TREK cell reduction for rhombohedral cells.
  • Fixed problem in d*TREK strategy always writing full omega range limits rather than user-specified range for strategy scans written to output header file.
  • Fixed problem in dtcell where a transformation from triclinic to monoclinic C uses the wrong transformation, and then reports a cell that is not even consistent with the (wrong) transformation used.
  • Revised message printed in in REQAB output from error to warning for messages printing "Error - Identity matrix not found for setting <n>".
  • Fixed problem with d*TREK crashing in Cnonunf whenever this object is initialized with a non-uniformity type (e.g. Simple_mask) but non-uniformity keyword field string is an empty string. Fixed by preventing further processing if such a condition is found in Cnonunf. Also fixed Non-uniformity dialog in CrystalClear from allowing such a condition to be passed on to d*TREK.
  • Fixed problem with batch restrain failing in dtscaleaverage whenever number of scans processed exceeded 9.
  • Fixed absorption correction crash in d*TREK when there is a "bad" batch in the dataset.
  • Fixed problem in d*TREK where absorption correction did not allocate enough memory in some cases, when the number of batches was more than 300.
  • Fixed problem with subset of orientation angles not being calculated correctly when indexing a rhombohedral cell.