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What's new in CrystalClear™ 1.4.0 

New Features

• Support for the new SCXmini instrument to provide a single integrated package for small molecule crystallography. This mode of CrystalClear operation contains the following enhancements:
  • Structure solution and refinement based on well-established SHELX structure programs SHELXS and SHELXL using a modeling program called System-Y to perform complete structure solution. Structure solution by Patterson and direct methods is accomplished with SHELXS and structure refinements are performed using SHELXL. Space group determination uses PROCESS package used in Rigaku's CrystalStructure™ package.
  • Powerful molecular viewer dynamically displaying System-Y modeling steps as they are processed and for post-structure manual refinements and molecular manipulations. The molecular viewer is based on the same molecular viewer used in Rigaku's CrystalStructure package.
  • Automatic and manual image collection, cell/HKL processing, and structure determination with simplified dialogs and setup procedures.
  • Find and index refelection operations performed using d*TREK® and all subsequent processing operation performed using FS_PROCESS processing suite.
  • CIF output and other structure results placed in its own sample subdirectory.
  • Setup and optimized for simplified SCXmini X-ray source, goniometer, and Mercury 2 detector hardware.
• Support for the new d*TREK 9.7 processing package.
• Support for the upgraded TwinSolve 1.67 processing package for twinned crystals which now includes support for the Rigaku Kappa goniometer.
• Dramatically increased speed for d*TREK processing server using optimized MSCSServProceDTREK.exe.
• Support for the Rigaku Kappa goniometer and new Saturn 724+, Saturn 944+, and Mercury 2 detectors CCD detectors
• Updates to the image viewer including new circle masking and middle mouse button support for dragging operations
• Updated Instrument Servers (CCD, R-AXIS, and RAPID) with support for new hardware options
• Incorporation of XML database file generation allowing ASCII text editing/viewing of program default parameter databases
• Improved CrystalClear server interface to Director with support for the multiple-scan strategy now supported in d*TREK 9.7.
• Expanded support for the separate JXG X-ray generator control, including a new pre-collection JXG script running mechanism.
• Incorporated still image collection capability.
• Updated/improved collision detection XML files for various instruments
• Updated site defaults for all instruments.
• Increased precision in wavelength values (up to six decimal places) displayed and used in CrystalClear processing.
• Expanded configuration file control for various CrystalClear operations.
• Improved support for Japanese character display when using Japanese Windows OS.
• Implemented FS_ABSCOR absorption correction algorithm as alternative to the Jacobson REQAB algorithm.
• Improved CIF file generation and versioning.
• Improved InstallShield installation and setup.

Enhancements

• Updated release notes.
• Incorporated a CrystalClear 1.4.0 Quick Guide documentation file in installation.
• During installation, automatically setup the DTREK_REFLN_BINARY system environment variable with a value of TRUE to create/handle d*TREK binary reflection files for a significant speed enhancement.
• Implemented a conditional install of the CrystalStructure and molecular viewer related components depending on whether SCX Mini application type is chosen during installation.
• Removed pre-collection warning dialogs for SCXmini and RAPID instruments.
• Fixed Number of spots for indexing in FS_PROCESS Index dialog to be 1000.
• Placed -nodaemon option for SCXmini instrument server options.
• PROCESS.exe has adjusted I/sigma I threshold.
• Updated values for distance, 2θ in SCXMini_RCD3.configuration file.
• Move SCXmini post-prediction prompt dialog display to lower right corner so that whole images can be viewed for predicted spots without manually moving dialog.
• Support for handling multiple settings on some spacegroups in the Parameters->Symmetry... dialog in SCXmini.
• Complete revamping of the Strategy dialog to handle the new dtmultistrategy multiple scan strategy in d*TREK 9.7 including expansion of the 2θ limits for the custom selection and validations to allow -2thetamax value to be selected on the larger swing side.
• Added automatic updates of the space group information during the typing of space group number and space group name in the Processing State Display and the Index Spots main tab dialogs.
• Added "on the fly" validations and value adjustments to all resolution minimum and maximum selection fields for the Find, Index, Refine, Predict, Strategy, Integrate, Scale/Average dialogs.
• Implemented operational support for several new instrument (goniometer/detector) types: 
  • AFC8 Saturn 724
  • AFC10 Saturn 724
  • AFC11 Saturn 724 Left
  • AFC11 Saturn 724 Right
  • AFC12 Saturn724
  • AFC12 Saturn944
  • AFC12 Mercury2
• Implemented FS_ABSCOR absorption correction algorithm as alternative to the Jacobson REQAB algorithm. Either can be selected in the Scale/Average dialog via radio buttons.
• Enhanced behavior of process-only strategy: Goniometer limits dialog now always displays preceding strategy dialog. If goniometer limits are found in image header, these values are displayed, otherwise all zeroes displayed. Whatever user adjusts in this dialog (if any) become the working limits in the succeeding strategy dialog. Also fixed tabbing in strategy goniometer limits entry.
• Implemented Visual C++ 8.0 compiled and optimized release mode version of the d*TREK server MSCServProcDTREK,exe along with its supporting dll files.
• Implemented circle masking cursor in the image viewer to show a circle rather than a radius line.
• Implemented pre-collection JXG script mechanism to allow X-ray operations such as generator ramp-up to be performed before starting scan collections. Implemented application.configuration file settings to support this mechanism.
• Enhanced handling of zipped files to not display a DOS console window everytime a zipped image is opened and unzipped. Also, CrystalClear will now automatically unzip zpped images in image directories if they have not already been unzipped.
• Implemented mechanism to produce a Fourier Fo/Fc file four.dat that allows all operations under Utilities->Analyze LS Results to be operational in SCXmini.
• Incorporated TwinSolve version 1.67 which has support for the kappa goniometer.
• Modified displayed picture on the image viewer navigation arrow toolbar buttons to distinguish from the window navigation toolbar buttons located on the mainframe toolbar.
• Implemented a GUI mechanism to help prevent user confusion over fact that most Setup sheet tabbed dialog parameters can only be saved to the Sample level defaults. This mechanism involves displaying a messagebox just before the Defaults Manager dialog is displayed noting which parameters can only be saved to the Sample level defaults. This dialog only will popup if the Save button is clicked (not the Run button) and only if the application is not in auto mode or Director-server mode.
• Implemented new splash screen graphics developed by the RAC graphics department for the macromolecular and small molecule versions of CrystalClear.
• For CCD instruments, implemented mechanism to obtain user-specified anode wavelengths using values obtained from MSCServDetCCD.configuration file supported in updated CCD server.
• Increased wavelength display/entry precision to at least six digits to right of decimal point throughout CrystalClear.
• Added menu item to open Reciprocal Lattice Viewer to CrystalClear View menu. Before, it was only accessible from a toolbar button.
• Widened field display for "Automatically accept best possible completeness/redundancy" on d*TREK Strategy main tab dialog.
• Enhanced failure messages resulting from processing server generated errors to display the server name generating error (e.g. "d*TREK") and the logfile name to examine for further details (e.g. "dtFind.log").
• Support for phi rotation axis in d*TREK Strategy dialog and dtmultistrategy command.
• Enabled immediate updating of empirical formula and expected volume within molecular formula field edit finished event wherever this field is found.
• Enhanced method of warning user that daemon server must be running when switching from a process-only task to a collection task in simulation mode.
• Generated CIF files are now versioned like log files and other files produced by CrystalClear.
• Added processing suite name (d*TREK, TwinSolve, FS_PROCESS) in Setup dialog title bar.
• Implemented error reporting in XML parsing code when reading/writing XML database files.
• Enabled rubberband operations in image viewer using middle mouse button in addition to existing right mouse button.

Bug fixes (CrystalClear)

• Many site default changes for various instrument types.
• Fixed error with predicted spots positions in FS_PROCESS.
• Fixed problem with Mo radiation being set to synchrotron radiation in SCXmini.
• Fixed problem with parameters in SCXmini Setup dialog not being saved on close.
• Fixed problem with modifications being saved in Scan State display or Collection dialogs when closing with system menu X button.
• Fixed bad formatting for Twinsolve Spacegroup Check Results dialog.
• Fixed problem with the FS_PROCESS resource.dat not getting the current distance, 2θ, and χ values from the SCXMini_RCD3.configuration file.
• Disabled the auto-run on the SCXmini Setup dialog if in a Process only task.
• Fixed Rank Crystal dialog allowing selection of multiple images from even separate scans as long as the scan template and basic collection parameters (e.g. distance, 2θ, beam center, etc.) are identical.
• Fixed argument keyword for TwinSolve DD command for AFC12 instruments.
• Fixed problem with texray.inf sometimes not being written when in SCXmini operation mode.
• Fixed problem with post-collection JXG script mechanism not working for schedules with two or more scans.
• Fixed problem when opening new sample as process-only and an inappropriate set of images was being offered due to presence of .log files in image directory.
• Fixed problem where changing the kV or mA setting in the X-ray source tab and then click either OK or CLOSE caused CrystalClear to crash.
• Fixed problem with still images not being able to be collected in CrystalClear and implemented necessary command parameter to allow user specification of the number of still images to take.
• Fixed problem with strategy schedule and associated scans being properly transferred to Collect Images dialog when saving a strategy schedule in a previous sample.
• Fixed problem in the FS_PROCESS Find Spots dialog where the user can either click "threshold" or "sigma" and the value boxes do not activate or deactivate as the user changes from one to the other.
• Widened mainframe Task combo box to show the full "Screen Collect and Process" text selection.
• Fixed SHELXL crash when running single-step refinement (post-SystemY modeling) on certain datasets in SCXmini mode.
• Fixed problem with molecular viewer toolbar button not resetting when closing an existing molecular viewer frame with either Close menu item or system close X button for SCXmini.
• Removed default redundancy check in SHELX refinement dialog for SCXmini.
• Removed automatic Fourier data file (four.dat) creation from post System-Y modeling sequence. It now is created upon demand from the functions that need it as input.
• Removed bogus second argument (a 0.0 value) to FVAR instruction in shelxl.ins instruction file during SCXmini structure determination.
• Incorporated fix for SCX mini operation mode where any ACTA instruction present in the input shelxl.ins file used by SHELXL to eventually produce a Fourier data file (four.dat) was removed. If the ACTA instruction was present along with the L.S. 0 instruction SHELXL would not produce a shelxl.res output file which interfered with the logic to produce four.dat, namely causing an infinite loop and hanging CrystalClear.
• Fixed menu-driven Rank Crystal command to 1) put correct resolution limits on dtranker command line, 2) use the first selected image file of the first selected scan amongst all valid selected scans as input to the dtranker command vi the "image = " instead of using the input.head header file, and 3) assign the To Use to be full image sequence range of the first scan ONLY if no image sequences among all scans have been selected.
• Fixed erroneous disabling of View Crystal toolbar button and menu item for a collect task.
• Fixed loophole where the abort server StopInstrument.exe could erroneously be started in a process-only task and lead to use confusion especially when running as a second instance of CrystalClear alongside a collect tasked instance.
• Fixed application.configuration settings to be compatible with old RMailer installation RMailer10sp1.exe. The new RMailer installation that comes with StructureStudio 2.0 Utilities cannot at this time work with CrystalClear. For those users that want to use the RMailer utility, they must install the old RMailer installation using RMailer10sp1.exe.
• Fixed following Director interface bugs: 
  • Fixed Director interface to ensure "_screen" is removed from collection scan templates for either recipe schedule collection scans or strategy result scans.
  • Fixed Director interface to ensure distance and 2θ values either recipe schedule collection scans or strategy result scans correspond to those specified in the Director-provided recipe.
  • Fixed Director interface to ensure the image width specified in recipe is used for strategy-produced scans rather than the strategy dialog database image width used in normal CrystalClear client operation.
  • Fixed Director interface to ensure strategy scans requested by Director are based on the recipe collect schedule scans and not on the recipe screen schedule scans (unless the recipe collect schedule scan is unavailable). This ensures that such things as exposure time come from the recipe specifications for the collect scans and not from the screen scans.
  • Fixed problem with Director-specified dtranker command line getting image = option set on command line instead of header = option effectively preventing ranking from Director. The image = option where an image is used to obtain specific parameters is reserved for manual-mode dialog-driven ranking. The same syntax flaw also put dialog-driven options for beam position, distance, and 2θ erroneously on the command line.
• Fixed abort progress dialog to now be system modal so that it always appears on top of other windows and is stringently modal.
• Fixed reciprocal lattice viewer crash found in the Display Options dialog.
• Made population of Space Group Results synchronous from d*trek server fixing problems with asynchronous behavior arising from from apparent problems of relative timing between CC and new speed-enhanced d*trek server.
• Fixed Laue Check table selection problem where the correct cell was not obtained due to lattice type not being in selection string. Also fixed the user responses not being printed in the dtcell log file when run from CC.
• Fixed problem with configuration file where parsing unbalanced left/right curly braces cause problems both in reading and writing configuration files. Problem was especially critical when writing as it would leave an empty, zero-length configuration file.
• Fixed problem where mask files created by user were erroneously retaining the base image's non-uniformity settings (<Det type>_NONUNF_INFO and <Det type>_NONUNF_TYPE). Both settings are now set to "None". Among other things, this fixes problem where the resolution values were not properly being updated in the image viewer upon selecting pixels.
• Fixed behavior of default showing of certain columns in scan table controls. This included showing the Step column by default for screen scans but hiding for collection scans. It also includes hiding by default the Completeness column for all scans.
• Fixed default reflection file selection ordering for the small molecule Final Refine Cell step dialog.
• Fixed problems related to reading UserPrefs_140.ho resulting from a schema update due to mismatching database schemas for the UserPrefs and ScanUserPrefs Hobjects that are embodied in the UserPrefs_140.ho file. Main problem was that after correcting and writing the corrected UserPrefs_140.ho file, the schema in memory was not being reset by reading back this schema before assigning database values. The effect to a user was that after installing CrystalClear 1.4.0 and opening any previously created user account from an earlier CrystalClear version, a crash would occur. Once this happened, the corrected file was already written and subsequent accesses to this file worked properly. Hence, it would do this once per new user accessed.
• Fixed problem when assigning default dtpofit<n>.ref reflection file for the small molecule mode Final Refine Cell dialog. Logic error resulted in an infinite loop effectively hanging CrystalClear.
• Fixed crash which occurred whenever current sample scan's distortion type was NULL and was being compared to the distortion type returned from instrument server when opening Image Collection dialog.
• Fixed crash which would occur whenever the instrument server was aborted by user and then user clicks the red X next to collection flowbar button a second time while abort confirmation dialog from first abort activation is still shown. Problem was that a boolean indicating an abort is in progress was not being set when clicking the red X (it was being set when clicking the toolbar Stop button or the StopInstrument.exe Stop button). This boolean flag prevents attempting to display a second modal (now system modal) abort confirmation dialog leading to the crash.
• Fix CrystalClear to recognize and handle "ServerClosed" commands originating from instrument servers and to display any possible error messages passed in these commands. Because the "ServerClosed" command was not registered as recognized command, when one was passed, the Tcl interpreter issued a cryptic warning message: invalid command name "ServerClosed". Now, if the "ServerClosed" carries an accompanying "ErrorMessage" Tcl option, this much more useful message now gets displayed. If no"ErrorMessage" option is found, nothing will be displayed.
• Fixed macromolecular site default files for AFC11, AFC11K, and AFC12 instruments to use Spherical 4, 3 as default choice for REQAB method in Scale and Average dialog.
• Fixed JDTPlot to close dtscaleaverage.log input file when it has finished plotting. This fixes problem with dtscaleaverage.log not being written correctly when second and subsequent invocations of the d*TREK Scale and Average command are made and JDTPlot is used to plot results. (Caveat: See next bulleted item).
• Fixed bug which causes JDTPlot display problems for d*TREK Scale/Average step results whose dtscaleaverage.log input file contained dashes in certain output tables by providing an updated jdtplot.jar. The previous version of jdtplot.jar did not have this problem, so we reverted to old file. Doing so, however, undid the fix made in jdtplot.jar for the problem where it was impossible to display multiple concurrent instances of JDTPlot when launched with the newest Java Runtime Environment (JRE) version 1.6.0 (see previous bulleted item). Multiple concurrent instances can, however, be produced by JRE 1.5.0 and earlier. A patch fix was made to allow user to specify the JRE executable he wishes to launch JDTPlot with via an application.configuration parameter called JDTPlotJavaPath. With this solution, user can have both version 1.6 and earlier versions on same PC. He then just specifies an earlier version if he wants the ability to display multiple concurrent versions. Only one JDTPlot instance at a time can be open when launched from JRE 1.6. A description of this problem is documented in the installation release notes.
• Fixed problem with clicking Cancel button in Laue Check dialog erroneously updating to selected spacegroup.
• Fixed problem where, if collecting with RAXIS, RAPID, or HTC instrument servers, the NumImages option of CollectImages command was being used to determine number of images to collect. This normally gets set to be the number of initial scheduled images for a scan, but if collection was aborted, the number was not adjusted to be remaining number of scheduled images in the scan. This resulted in "excess" images being collected and a nasty error being reported.
• Fixed problem where a file named "Program" or "Program.exe" located in the Windows root directory C:\ caused spawned servers using CreateProcess API call to fail.
• Fixed bug where an erroneous message is displayed using RAXIS-based instruments indicating distance limit values are not found in input header when trying to run Strategy. Fix was to include this validation for all instruments, not just CCD instrument server where it was formerly being done.
• Fixed bug where red X button extension for Collect Images flowbar button was disappearing whenever another processing step dialog was opened and then closed.
• Fixed bug where starting a new scan collection of a given distance after aborting a previous scan collection erroneously used the previous scan's distance. The problem was that old distance "axis" name submitted in the CollectImages command was "TransZ/Dist" instead of new name "Distance" recognizable by HTC and RAXIS instrument servers.
• Fixed problem dealing with not being able to recollect images in a scan where images already were collected using the "Schedule All" function in the scan table. Fix also applies to the "Set All", "Select Images...", and direct manual editing of the Scheduled column. A further fix was to prompt user whether to reschedule or not to ensure images are not mistakenly overwritten.
• Fixed a bug that could lead to a crash if a normal error in the Determine Structure function (in small molecule or SCX Mini) was encountered.
• Fixed crash problem resulting from opening an active mask image file.
• Fixed bug dealing with Laue Check step getting stuck if two or more No answers are given to the "Do you want it reindex?" prompt.
• Fixed angstrom symbol display in Japanese OS throughout CrystalClear.
• Fixed behavior in Laue Check where if selecting No to the "Do you wish to re-index to find unique? prompt, the reindexed cell dialog was still being shown.
• Fixed format in CIF generation code to support six decimal precision wavelength. texray.inf already supported it.
• Enhanced method of warning user that daemon server must be running when switching from a process-only task to a collection task in simulation mode.
• Fixed problem where if the length between crystal and detector is the out of datum position, the detector automatically returns at the datum position and changes the omega angle in the manual menu of "Raxshape".
• Fixed problem where image viewer font set in User Preferences was not being updated to any currently opened images.
• Fixed problem in FS_PROCESS Predict Spots dialog where box size did not change in "Toggle Filtering" and default box size was too large after second image.
• Fixed text display problems in Japanese OS for Run, Close, and Save buttons of the FS_PROCESS Predict Spots dialog.
• Fixed erroneous behavior resulting from clicking the flowbar while the modeless "SCX Mini Cell Determination" prompt dialog is displayed.
• Hid Set Resolution Limits menu item in SCX Mini mode. This dialog which supports d*TREK resolution processing does not apply to all steps in SCX Mini mode, some of which are FS_PROCESS steps.
• Ensured the default for 2D processing checkbox to always be set in the Find Spots advanced tab dialog.
• Fixed problems dealing with FS_PROCESS Scale and Absorption step including the path of the location of the .fsq files (normally located in the sample directory)was wrong causing Scale and Average to fail.
• Fixed wavelength field in CIF to display up to six decimal place precision.
• Fixed crash resulting from resource.dat not being properly updated when doing face indexing in RAXShape in small molecule mode.
• Fixed problem with CrystalClear going into automode in small molecule mode upon exiting Post-RAXShape dialog.
• Incorporated updated factory default files matching latest Hobbit database schema.
• Implemented informational messages indicating which database .ho files are being read during a propagation of defaults operation. Besides the obvious utility of showing progress, this messaging will allow identification of corrupt database files in case a crash occurs while reading them. Also made an existing message more descriptive that gets written when a Hobbit .ho database file schema file mismatch is detected and is automatically corrected/updated. Again this message can be used to help identify problem files we may encounter.
• Implemented a simple mapping set by the Setup/X-Ray Source dialog Optics Type combo box to strings identifiable by FS_PROCESS when in this processing mode. Now "Confocal" sets the string "CMF" and "Graphite Monochromator" sets the proper value "graphite" into the monochromator material: filed of resource .dat.
• Fixed saving of JXG pre- and post-collection script filenames to all upper default levels (site, user, project). This was unavailable before.
• Replaced angle bracket characters ("<" and ">") with parentheses in the "(None)" and "(AutoSetPower)" choices available in the JXG pre- and post-collection script combo boxes of the collection dialogs. The angle bracket characters cause problems when written to the XML database files because they are special syntax characters used in XML.
• Disabled XML schema validation when reading XML database files that could cause crashes under certain circumstances. Schema validation when reading XML database files is really unnecessary in CrystalClear operation.
• Implemented error reporting in XML parsing code when reading/writing XML database files.
• Removed a no longer dialog control on the d*TREK Strategy dialog that caused a crash when accessed under certain circumstances.
• Fixed problem with display of characters in image viewer containing underline and strikeout characters when saving font in the User Preferences Miscellaneous dialog.
• Fixed an erroneous symmetry operator which affected dtscaleaverage results for space group 212.
• Fixed problem of a crash resulting from resource.dat not being properly updated when doing face indexing in RAXShape while in small molecule mode using d*TREK processing suite. This fix updates the d*TREK orientation matrix to FSP coordinates needed by RAXShape and writes the results to resource.dat. It also prevents reading the resource.dat back in for SM mode since rest of processing will be in d*TREK processing. The reading of the resource.dat was intended for SCX Mini mode where after indexing all remaining processing is done with FSP.
• Fixed Japanese OS font problems in SCX Mini Setup dialog and Setup Crystal2 tab dialog.
• Fixed problem in FS_PROCESS Index dialog where number number of peaks in macromolecular mode was being incorrectly obtained.
• Fix for message telling user to contact "Rigaku" (not "MSC") technical support if a particular instrument site default file cannot be found.
• Fixed when and how the FS_PROCESS resource.dat is initialized and written for small molecule and SCX Mini modes of operation. The resource.dat file is now written when the Setup dialog is displayed. Files are now initialized with proper scanner and goniometer definition information for current instrument to ensure RAXShape face-indexing works properly when running d*TREK processing in small molecule mode in CrystalClear.
• Fixed file I/O timing crashes that could occur during the d*TREK to FS_PROCESS orientation angles conversion operation when writing a resource.dat file suitable for RAXShape input when running d*TREK processing in small molecule mode in CrystalClear.
• Fixed problem with TwinSolve license mechanism not working for some very specific dongle IDs. Fix was to read the license file as binary to ensure control characters could be read from encrypted dongle ID key.
• Fixed problems in InstallShield installation:
  • Fixed problem in InstallShield where SCX mini related component files were not properly uninstalling during uninstallation via the Add/Remove program.
  • Fixed InstallShield installation to display a message indicating that the DTREK_REFLN_BINARY environment variable is being set. On occasion this can take awhile and leave user confused as to whether something is happening and whether the install is completed.
  • Fixed problem in a Repair operation where a possible user-selected application type was not copying the proper application.configuration file with the proper application type (MM or SM) if the user deletes or renames an existing application.configuration file.
  • Fixed problem during a Repair operation where the application.configuration file could not be read for application type forcing display of the prompt dialog for application type after the file moving/installation operation had already started. The dialog was displayed on top of the installation progress dialog and was not dismissed until the background file moving process had completed, giving the illusion the installation was hung. The fix involves temporarily halting the background file transfer process until user answers and dismisses the prompt dialog.
  • Implemented running of Visual C++ 8.0 redistribution DLLs using Microsoft install utility vcredist_x86.exe in the CrystalClear InstallShield installation now required to run the d*TREK release-mode executable compiled in Visual C++ 8.0 for speed.

Bug fixes (Instrument server)

CCD instrument server (MSCServDetCCD.exe ), version 3.9.0.1:

• Modified ACA demo options to not try kappa free rotation on +ve side of omega, as it will cause a collision on our instrument.
• Added getting of current hardware positions for crystal goniometer axes before checking movements before starting scan so that cases such as the AFC10 phi will be handled correctly if moved by external device.
• Added explicit check for collision at start of scan range when checking movement between scans.
• Added documentation for the DatumPhiBeforeCollection option.
• Changed error condition when checking range when moving through scan and improved error message.
• Added querying of hardware position for axis since it may have moved using other means.
• Added routine for writing collision detection object(s) as a XML file.
• Changed default d*TREK header DET_NAME to be CCD_ instead of UNKNOWN_.
• Added check to make sure that the start of a scan is not in a collision region. Made the error message for collision regions checks a bit more understandable.
• Added a query of the hardware position at the start of the scan for each axis, since some can be controlled by other mechanisms.
• Removed class's implementation of collision detection to use collision library. Class's implementationwas not being used, but the code was still around.
• Removed setting of collision detection objects, since not used now that collision library is used.
• Added routines for writing out collision detection object in XML.
• Added fix for problems when end of range is between steps used for determining ranges.
• Collision detetion object now written as a file in the current working directory and COLLISION_INFO for images written in that directory will point to it instead of the one in the installation directory.
• All logs and files are now written relative to the configuration directory rather than the CrystalClear installation directory, which causes problem for StructureStudio if CrystalClear is installed.
• Add support for interpreting "CloseShutter" directive (treated as an abort without aborting everything) during OpenShutterAndWait command.
• Added routines for creating new directory, and for checking if a file is a directory.
• Add support for interpreting "CloseShutter" directive during OpenShutterAndWait command.
• Configuration directory used rather than CrystalClear installation directory for various log files.
• Active mask is not embedded in direct beam shot images, since a bad pixel in the active mask could cause the direct beam to not be found.
• Added generator side to goniometer description in header
• Added copyright notice and updated file format
• Version string now always contains patch number
• Commands converted to use standard string of CCDCommandFinished.
• Added output of collision library version info.
• Added -nodaemon option for connecting to detector server without using daemon server.
• Reduced start speed for omega motor, based on problems with other kappas.
• Added merging of header before writing default header to avoid problem of bogus pixel size info written into default header.
• Added implementation for checking is scan speed is allowed. For now, kappas will be allowed to collect at speeds greater then start speed until omega motor problem is resolved.
• Changes for server changes that put DirectBeam shots and Attenuator factor shots in installation directory.
• Added check to make sure that AttenuatorFactor is actually a directory
• Modifications to Direct Beam processing routines
• Added routine for getting maximum time allowed in shutter open command.
• If direct move would fail due to collision, then distance is check to see if moving it back will allow the movement to occur.
• Added routine for returning if goniometer axis was motorized.
• Added collision detection library version numbering and routine for returning the version number
• Added configuration file option for supporting AFC8 attenuator.
• Added documentation on SupportAttenuator config file option.
• Updated documentation to describe setting refinement offsets via <Axis>Datum keyword.
• Updated copyright info.
• Added AFC11K goniometer
• Fixed bug in interpreting attenuator response for AFC8
• Updated Saturn944Default.header.
• Added routine for getting detector name.
• Added default routine for turning enclosure light on/off.
• Added GetInstrumentParameters as command that will be executed when an Abort is sent.
• Added support for SCXMini
• Added test around receiving image from detector to make sure that the detector read finished without error.
• Added support for non-zero 2θ and distance positions, for systems that have fixed non-zero 2θ/distance
• Added backup types of files to use when loading collision library, for goniometer/detctor types not explicitly found, but can be inferred from other types.
• Changed expose and read command to use triggers if available and to include a directory path in the name.
• Fixed bug where detector info was checking for valid crystal axis name instead of using detector axis name
• Added goniometer description.
• Added documentation for DatumPhiBeforeCollection option.
• Fixed bug in Collision Detection occurring if no bitmaps defined.
• Added a distance/2θ check to make sure that uninitialized values do not cause 2θ adjustment to happen.
• Added fix for setting rotation limits keywords to hardware values.
• Image Transfer via Sockets: Implement GetImageData command
• Still image capture: takes NumImages if ScanStart and ScanEnd are equal
• Bug fix: typo in Triggers = {on} configuration file statement closing brace was "]"
• Standalone operation mode: -standalone command line parameter
• Change default Omega axis start speed for AFC10 and AFC11 to 5
• Apply LogDirectory to command.log path; default -config path for log files if -log is not specified
• Implemented Phi scan for AFC12
• Fix bug in attenuator movement causing crash under Linux
• Change to Xerces library release build to eliminate dependency on MSVCRTD.dll
• Eliminate duplicate responses to "PD" command in simulation mode
• Add 0.5 to trigger delays in scan shutter open command to get rid of rounding error in the Linux build
• Add SCXMini to Linux build
• Fix bug causing active mask bitmap not to be applied in CollectImages command processing
• Fix bug causing warnings not being given if active mask files are missing
• Move responsibility for loading Active Mask bitmaps to detector server
• Implement Tcl command to detector server to obtain current active mask bitmap
• SCAN_SEQ_INFO in image header has the actual image number as its first value; HEADER_VERSION is changed to 1.1 after SCAN_SEQ_INFO is updated
• Relevant error message for Phi unlocked timeout ported from R-AXIS
• Improved log entries when collision bitmaps are read
• Added options to MSCServDetCCD configuration file to allow detector and crystal goniometer to be returned to default position after collect images
• Goniometer initialization default order changed to move detector first
• d*TREK library updated 
• Report collision incidents from collision detection
• Fix bug affecting overload image application, and d*TREK header updates related to RAXIS compression
• Add XML filename and position configuration to predicted error messages sent to client
• Handle out-of-range errors occurring in calls to collision detection
• Fix programming error causing dropped characters in Tcl commands
• Correct rounding of negative numbers
• Implement CorrectImagesForOverload command
• Fix client disconnect bug affecting non-standalone mode
• Add AttenuatorCode and AttenuatorType configuration file options
• Correct Omega datum position defaults for left port and right port on AFC11K and AFC12
• Replace axis code with axis name in limit switch error messages
• Fix bugs affecting AFC10 attenuator type and attenuator code options
• Fix bugs affecting AFC10 attenuator move and init commands
• Implement timeout for connections to daemon and detector server - log message and notify client
• Fix header error reporting when getting image from detector
• Add axis name to collision and limit switch error messages
• Add instrument status updates during dark image collection
• Fix bug in CollisionDetection
• Update to keyword/value parsing
• Put actual expose time in d*TREK header of saved overload images
• Implement OverloadAutoSwitch option
• Implement automatic fallback mechanism for loading active mask bitmaps: unless old methodis configured, if GetActiveMaskBitmap command to detector server fails, the old method will be attempted.
• Modified warnings when loading active mask bitmaps to describe more clearly the nature of any error encountered.
• SCAN_ROTATION in image header has the actual image start and end angles; HEADER_VERSION is changed to 1.2
• "CopyrightInfo" added to Attenuator Factor and Direct Beam logs and summaries
• Increased Direct Beam plot size and added additional statistics to Direct Beam and Attenuator Factor logs
• Update source wavelength constants and increase SOURCE_WAVELENGTH numerics to 6 decimal places
• Update constants and implement configuration file options for source wavelengths
• Append overload correction bitmap to image file and add OVERLOAD_BITMAP_TYPE, OVERLOAD_BITMAP_SIZE header entries
• Enable collision check for AFC7 when checking collection time
• Log configuration file options to new log file after changing working directory
• Use SaveRawImages = Off | On option to save raw Direct Beam shot and Attenuator Factor images
• Fix bug in AbortCallBack function
• Apply smoothing to prediction in CalculateCollectionTime()
• Add MaxScanSpeed = #.# to GetCollectionTime response
• Add PauseCollection, ResumeCollection commands
• Write default header path and filename to log file
• Add TimeStamp to server connection established and failed notifications
• Fix bug in the overload correction applied when auto-switch is enabled
• Skip active mask checks when -nodetector is specified on the command line
• Add call to update UID immediately after sending scan command, to improve shutter open indicator response for short expose times
• Add attenuator type and attenuator code options for AFC8
• Apply active mask bitmap when calculating if overload correction is needed
• Fix memory leak introduced in OverloadCorrection class affecting version 3.8.7.0
• Test image header for presence of RAXIS_COMPRESSION_RATIO before applying compression
• Add check for RAXIS_COMPRESSION_RATIO before applying compression to image
• Extend recovery option to permit AFC12 kappa movements without collison errors
• Fix error message reporting in GetCollectionTime command
• Fix overload raw image filename keyword/value sent to detector server
• Add support for compressed 18-bit images
• Add OverloadBufferWidth config file option; set pixels in buffer zone to overloaded value

RAXIS instrument server (MSCServDetRAXIS.exe ), version 3.4.4.0:

• Added additional output when changing directories
• Fixed error in assignment of data transfer type.
• Added peeking at config file to determine if instrument uses PCI for data transfer before assigning axes, since that information is used when setting up axis information.
• Reversed order of assigning axes and reading config file so that axis information is read from configuration file.
• Added output of axis min/max/datum/default position options applied from configuration file.
• Added erasing of plate before doing single plate data collections.
• Added moving the IPs to the ready/erase position after collection of dual plate collections.
• Added support and updated documentation for pixel jitter
• Added new ramp table and datum commands for distance axis
• Made changes for working with new PCI card driver
• Added # parameters error when datuming read head X axis to list of errors recoverable by a resend.
• Increased number of chars read at one time to 63.
• Added additional Directbeam information to log file (candidate peak listing, ranking).
• Added reinitialization of Direct Beam summaries before evaluating.
• Fixed potential bug in checking for end of command if sequence is more than one character.
• Added erasing of single plate image collection before collection starts
• Update copyright notice and version string formatImage Transfer via Sockets: Implement GetImageData command
• Still image capture: takes NumImages if ScanStart and ScanEnd are equal
• Fix pixel jitter between odd and even images
• Revise CE Mark error warning when rotating IPs
• Standalone operation mode: -standalone command line parameter
• Bug fix for problem loading simulator images
• Apply LogDirectory to command.log path; default -config path for log files if -log is not specified
• Fix duplicated analysis data logging for two-plate systems
• Bug fix: ABORT does not abort data collection quick enough; shutter stays open (R-AXIS IV)
• Fix programming error causing dropped characters in Tcl commands
• Correct parsing of string in in R-AXIS IV++ shutter state response to solve erroneous shutter closed status reported during Oscillate command
• Fix client disconnect bug affecting non-standalone mode found by Yasukawa in MSCServDetRAPID
• Fix axis options from config file being ignored for RAXIS IV++ χ
• Adjust read head X-axis speed for 50um resolution (not confirmed that this is valid)
• Fix bug in renaming temporary image files: a file was not created if the filename contained spaces
• Fix error report in writing image header
• Implement FirstReadChunk R-AXIS II configuration file option (for service personnel)
• Correct device type for IV++_Distance (was reporting IV++_Chi)
• Implement still image capture sequence using NumImages = # in Collectscan command
• Replaced instances of "can not" with "cannot"
• Fix bug in UpdateInstrumentDisplay file updates for Expose
• Add AllScanFinish = # to UID
• Log full header to log file after changing working directory
• Fix bug in AbortCallBack function
• Add PauseCollection, ResumeCollection commands
• Correct NumImages calculation in scan collection
• Recognize old detector axis names in GetCollectionTime and CollectImages commands from CC
• Add periodic check for shutter status during image collection in DirectBeam and CollectImages (awaits RCD3 modification to complete)

RAPID instrument server (MSCServDetRAPID.exe ), version 2.1.1.1:

• Implements MoveCrystalToDefaultAfterCollection configuration file option
• Fixed initialization of ReadHeadZ<XXX> Positions
• Implements still image capture
• Fix bug in UpdateInstrumentDisplay updates for still images
• Add AllScanFinish = # to UID
• Correct NumImages calculation in scan collection
• Add PauseCollection, ResumeCollection commands

HTC instrument server (MSCServDetRAXISHTC.exe ), version 2.2.3.1:

• Implements still image capture
• Fix bug in UpdateInstrumentDisplay updates for still images
• Add AllScanFinish = # to UID
• Correct NumImages calculation in scan collection
• Add PauseCollection, ResumeCollection commands
• Recognize old detector axis names in GetCollectionTime and CollectImages commands from CC

Bug fixes/enhancements: d*TREK (version 9.7)

• Implemented a new multi-strategy in a new module called dtmultistrategy which automatically selects the best multiple scans and detector positions for optimal data collection. A special Collision Library determines collision-proof rotation ranges.
• Implemented crystal ranking to help users screen crystals for collecting data from the best ones and avoid collecting data from the poor ones.
• Implemented speed enhancements including use of binary reflection files and compiler and code optimizations.
• Incorporated improved algorithms for indexing, scaling, and space group determination.
• Fixed a reporting problem when using a previously collected reflection file.
• Fixed an old bug when using rejected reflections in completeness/redundancy calculations.
• Improved algorithm for crystal goniometer hardware limits determination, when Phi is the rotation axis.
• Other specific fixes/enhancements by module:
  • All modules:
    • Changes to work with a cylindrical detector with crystal to detector distance not at center of cylinder.
    • Image filenames ending in .bz2 are assumed to be compressed with bzip2 and are uncompressed accordingly.
    • Bug fixes in the Creflnlist class and <itr> should help prevent bogus characters in the reflnlist files.
    • Changed copyright notice.
  • Most modules:
    • Updates to compile on the native Solaris CC compiler.
    • Changes for double vs float functions.
  • Many modules:
    • INFO messages at end of output suggest which step is appropriate next. This is to guide new users in the steps to take in case they do not have a manual handy.
    • Fixed problems arising from using a new compiler.
    • Much faster now on some Windows computers.
  • dtcell:
    • Changes to label a Laue class as a poor choice.
    • Fixed a bug in Laue check when dealing with monoclinic cells with beta approximately equal to 90 and b-axis shorter than a-axis.
  • dtindex:
    • Disabled multiple debugging messages in dtindex triggered by some wrong input.
    • Verified dtindex returns failure when it fails to index.
  • dtintegrate:
    • Update to do a better job profile fitting of spots that are close together.
    • Axial reflns are now written as *axial.ref and not *zone.ref.
    • New -differentscan and -differentdet command line options.
    • Log file changed slightly.
    • File of h00, 0k0, 00l reflections zone.ref named axial.ref now.
    • Update to do a better job profile fitting of spots that are close together.
  • dtmultistrategy:
    • New program for data collection strategy with multiple detector positions, including automatic distance and multiple 2θ generation, as well as support for collision information (XML-based).
    • Incorporated collision detection routines.
    • Command line options to specify scans with different crystal goniometer angles to test.
    • Flexible tolerances.
    • Overlap checking.
    • Output .head file has new keywords with the scans selected by dtmultistrategy.
    • Fixed a problem in dtmultistrategy which occurred when Collision library generated more than one collision-proof range per set-up.
  • dtprofit:
    • Update to do a better job profile fitting of spots that are close together.
  • dtpredict:
    • New -differentscan and -differentdet command line options.
  • dtranker:
    • Enhancements to the Rules dealing with the resolution shells, reflection sharpness and mosaicity.
    • New options to skip image processing steps and/or disable selected ranking rules.
    • Multiple images now accepted via the sequence=... option.
  • dtrefine:
    • Changes to remove overlap-flagged reflns from refinement.
    • Fixed a bug in dtrefine: -sigma value is ignored when refining "from images" and a default value of 10 is used instead.
  • dtscaleaverage:
    • Changes to label a Laue class as a poor choice.
  • dtstrategy:
    • Incorporated collision detection routines.