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What's new in CrystalClear™ 2.0 

New Features

Small Molecule Modes

In additional to the standard macromolecular mode of operation, two additional independent modes of operation geared toward small molecule applications have been incorporated.

SM-Auto is a fully automatic mode designed for use only with the integrated SCXmini and XtaLAB mini instruments using a standard processing sequence using d*TREK for finding/indexing reflections and FS_PROCESS for integration and scale/average operations.

SM-Expert optimizes support for small molecule collection and processing for all available supported instruments and allows full CrystalClear user interface access and control (where all command dialogs are displayed and operated via manual flowbar operation).

Small Molecule Automatic Structure Determination

As a final step, both small molecule modes include a new step for automatic structure determination. CrystalClear 2.0 automatically prepares a CIF file and spawns CrystalStructure 4.0 to automatically determine the structure.

New Directory Structure

Newer versions of Windows limit access to C:\Program Files, so programs, configuration files, documents, log files etc are now stored in a C:\Rigaku directory. This allows CrystalClear to be run either as an administrator or a normal user. Only a single instrument configuration file is now installed to match the actual instrument being used. The installation procedure can automatically update the configuration files with values from CC140, CC136, and CC135.

Processing Package Improvements

CrystalClear 2.0 includes d*TREK version 9.9.8.4 with many improvements and bug fixes. For small molecule work, there are also many improvements to Fine Slice Process (FS_P) and TwinSolve which is now at version 1.83. The processing packages have also been optimized for speed and the performance has been improved considerably. The plotting features have been improved and it is now possible to plot the results of FS_P.

New Macromolecule Spot Chasing Default

Processing results for macromolecule data may differ for CrystalClear 2.0 vs. CrystalClear 1.4 because the integration spot chasing option has been disabled by default. Spot chasing is still enabled by default for small molecule processing.

The integration spot chasing option directs the underlying d*TREK processing engine to offset the integration domain on a reflection by reflection basis to better match calculated and observed positions. CrystalClear 2.0 makes it easy to integrate reflections either way as shown in this screen shot (unchecked "Spot chase mis-predicted spots" is the macromolecule default):

The spot chasing option has been disabled by default for macromolecule processing because doing so was found to decrease R_merge on average over a "representative" collection of protein datasets. Your results may vary! In particular, for twinned or closely spaced reflections it is often best to turn spot chasing off in order to avoid the possibility of contamination by nearest neighbors. On the other hand, for high quality macromolecular data (sharp, well-separated reflections) the best choice is often to turn spot chasing on. Note that spot chasing was turned on by default when d*TREK integration was invoked from CrystalClear 1.4.

We encourage you to take advantage of the new flexibility built into CrystalClear 2.0 to reach your own conclusions regarding spot chasing.

Support for new Hardware

CrystalClear 2.0 includes support for the XtaLAB mini, the new 18 bit (+) CCDs and other new hardware.

• AFC10 SATURN 724+
• AFC11 SATURN 724+ Left/Right
• AFC11 SATURN 944+ Left/Right
• AFC11K SATURN 724+ Left/Right
• AFC11K SATURN 944+ Left/Right
• AFC12 SATURN 724+
• AFC12 SATURN 944+
• XtaLAB mini MERCURY3
• CLK SATURN 724+ (CrystalLogic Kappa goniometer)
• SinglePhi A200
• SinglePhi A200 Motorized Dist
• SinglePhi SATURN 944+
• SinglePhi SATURN 944+ Dist

Other New Features

• Updated and much improved user manual
• It is now possible to pause and then resume data collection. You can also stop after the current image so that you do not have to re-initialize.
• The X-ray control has been enhanced and support has been provided for the SCXmini and XtaLAB mini. This included facilities to update distance and 2- Theta values based on results for a standard sample.
• Improved reliability of sample files
• Better logging of updates and other activities
• The image viewer allows additional display parameters to be saved as user preferences and will write the image as a JPEG format file. It also allows the user to control color coding for masked and saturated pixels.
• Mask file generation and recording improvements including masking support for FS_P.
• Better control of overload correction.
• Better control of scan image numbering.
• Improved axial photos.
• Much improved CIF files
• Many bug fixes and minor enhancements that make CrystalClear 2.0 easier to use and more reliable.
• The installation includes a detailed set of release notes that give more details on the enhancements and bug fixes.

Database Corruption Problems

CrystalClear keeps sample and default information in binary .ho files. Since these files can occasionally become corrupted, we also keep this information in a text xml file. But since the text xml file is so large, it is impractical just to read it each time. We plan to eliminate binary .ho files entirely in the next version of CrystalClear and we have fixed most of the problems that caused them to get corrupted in 2.0. But there may still be problems as your samples get updated from previous versions. Unfortunately since these are binary files, the problems usually result in a crash.

If you are updating from CrystalClear 1.4.0 it is usually possible to recover using the following procedure.

Determine which .ho file is causing the problem

1. If this happens when propagating defaults, you can look at the CrystalClear log file in the C:\Rigaku\Log directory. The last file in the log file is usually the culprit. 
2. If CrystalClear crashes when you start up, it is usually the current sample's ho file. But it can also be a default file. So try to start CrystalClear a second time. 
3. If neither of these works, look in the release notes for a more detailed diagnosis process.

Delete the bad .ho file 

If CrystalClear does not find the .ho file, it will look for the corresponding .xml file. The xml file is usually OK, so just deleting the .ho file will often fix the problem. If you are not sure which .ho file is bad, delete all of them you suspect. It will take longer to start up, but it should still work.

Restart CrystalClear

If this does not work, see the release notes for more detailed instructions.