Crystal-Clear 1.4.0 Notes

Double click Crystal Clear icon to begin crystal evaluation

There is no password required to activate the program.

Select the project name or create a new project if needed. Make a new sample name for a new

crystal. This will insure that you don’t overwrite previously collected data.

If you are working on a new sample, select TASK as Screen Collect and Process. If you

want to go back and work on an old data set, select TASK as Process. If you wish to restart an

older data set without using previously determined unit cell information, select the new sample

box, rename the sample but using the browse button, select the directory containing the original

data. This is useful if you have failed to get an adequate integration and want to reset all the

default parameters. You can process a data set while the instrument is collecting data by

selecting Process as the Task.

Select the Processing Suite desired. In general, d*trek is used initially to determine the

unit cell and set up the data collection parameters. For data integration, fs_process usually gives

better results.

If you selected Screen Collect and Process, you will have to initialize the instrument

before starting. If the blue cube in the upper right corner of the display is rotating, all is well.

Initialization will take about a minute. Occasionally, the instrument will not respond. Try

closing some of the command windows relating to the detector. These are located on the bottom

of the monitor along the horizontal task bar.

Steps that need to be taken are listed in order on the left side of the display.

SETUP orients the instrument so that you can easily mount the crystal and begin crystal

alignment.

You can enter data collection temperature (-173 for the Saturn and the Mini). In menu Crystal1,

you can enter the crystal size, color and morphology.

Click OK and the alignment menu should come up. The video camera will be displayed along

with the Crystal Shape Measurement tool.

Under the MEASURE drop down menu, select TAKE PHOTO to bring up the goniometer drive

control routine. For the Saturn, set omega to 20.0, chi to 0.0 and phi to 10.0.

Align your crystal by moving phi in increments of 90 degrees. It is a good idea to get the

crystal height set early in the process. Check the alignment by noting the crystal position at phi

angles 180 degrees apart (for example, 10 and 190 degrees, and 100 and 280 degrees on the

Saturn). The crystal is aligned if it is in the same position relative to the cross hairs at the

extremes of each scan.

For oddly shaped crystals, this can be difficult. The idea is to align the center of mass of

the crystal as close to the center of the instrument as possible. The unit cell is determined by the

position of the reflections on the CCD assuming the source of these reflections (the crystal) is

stationary.

Once the crystal is centered, close the Crystal Shape Measurement display and move to

INITIAL IMAGES.

The Rigaku instruments use omega scans for data collection. The Det. Dist. is fixed for

the Spider (127.4 mm) and the mini (50.0 mm). This value can be changed on the Saturn with

the default value set to 45 mm. Minimum distance is 40 mm. Maximum distance is 115 mm.

The start angle and end angle values refer to omega settings. Width is the width of the scan for

an image. Step is the angular separation between start angles for consecutive images. For

contiguous scans, the Width and the Step values should be the same. Num Images is the number

of images collected. Ten images is usually sufficient. If you ask for more, you may have to

reduce the value of Step so that you don’t exceed the permissible range for omega. An alert

highlighted in YELLOW will appear with an error message. Reduce the Step value until the

range is acceptable. Exp Time is the time in seconds each image is exposed to X-rays. This

value is highly crystal dependent but a good guess is at least 25-45 seconds. The total scan time

will be listed in the Time Estimate field. 10-15 minutes is not too long for an average crystal.

A few extra minutes at this stage is time well spent. The structure determination and

refinement depends on having a good quality crystal, with data collected in a well thought out

process. Spot shapes should be approximately oval. Elongated spots due to long needles are not

unusual but beware of excessive streaking. Clusters of spots around a single intense spot may

indicate that you have a twin or a multiple crystal. Look carefully at the cell refinement results.

Note that the Rigaku strategy uses a large change in omega between scans (Step value). This

will allow you to explore a greater range in diffraction space in a short period of time. The

disadvantage is that you miss information on the crystal mosaic character.

After collecting the initial frames, the FIND-SPOTS routine will come up.

The default conditions are generally OK. Crystal_Clear will search all the intial frames looking

for reflection positions.

Once the search is complete, the INDEX SPOTS menu will appear.

The user chooses solution check box should be selected. Under space group, the unknown

button should also be selected. In addition, if there are problems with cell determination, you

can select the Advanced button to make some changes in the way d*trek finds the unit cell.

Select the diffs button, to use difference vectors between reflections. It is another way to get a

starting orientation matrix. Also, if you know the unit cell from a previous crystal, you can enter

the unit cell parameters and have d*trek fit the reflections to the ‘known’ cell. But always check

that the predicted spot positions match the observed positions using the Predict Spots routine.

If you have to go through selecting the Diffs button or entering a known cell to index your

reflections, you should consider choosing a new crystal. Autoindexing with a good crystal is

usually routine.

Once you are satisfied that you have a suitable crystal, you must calculate the data collection

strategy. The default data collection strategy used by Crystal_Clear will doesn’t yield a strategy

that produces a complete data set. You should always add framesets or increase scan ranges to

the strategy selected by Crystal_Clear.

Initially, you select the maximum resolution for data collection. Most journals require a

complete (98-99%) data set out to a maximum resolution of 0.84Ǻ. If the crystal scatters well,

set the maximum resolution to 0.77Ǻ. The higher you set the resolution, the more frames of data

will have to be collected. Given that you have a limited time to collect data, the more frames

you collect the shorter the collection time will have to be.

By default, the scan width for each frame is taken from the scan width used in the initial images.

Usually, the scan width is set to 0.5 degrees. For a good quality crystal, this value can be set to 1

degree. On the Spider, due to the much larger detector size, the scan width is typically 5 degrees.

Select run and Crystal_Clear will calculate a data collection strategy based on the maximum

resolution you have set and the symmetry of the crystal determined in the Assign Unit Cell step.

The above image is for the Saturn. The maximum omega range for the Saturn is from -110 - 70°

when kappa, , is 0. When is -60, the omega range (Start Angle), should be set to -100 and

the end angle to 22. When is 60, the omega range (Start Angle), should be set to -50 and

the end angle to 70. The default data collection strategy is NOT SUFFICIENT for a 99%

complete data set. Too often using the default settings, the data completeness is below 95%,

which will generate a CIF Alert. My suggestion is to use the default settings, but expand the

angular range to its maximum values for the given setting. Also, you need only one scan set

with at 0, with ranging from -110 to 70 because at set to 0, and are collinear.

When using the Saturn, some of the framesets will have χ settings of either -60° or +60° (or -70°

and +70°). At these χ settings, you will not be able to get the full omega range due to the

possibility of a collision. If you set an omega scan at high χ that can cause a collision, you will

see an error message appear highlighted in yellow. You won’t be able to collect data until you

clear that message by adjusting the scan range.

For data collection on the SCX-Mini, it is advisable to use three scan sets with set to 0, 120 and

240°, with omega scans set to the maximum range, -120 - 60°.

For all data sets on the SCX-Mini and on the Saturn, you should select the dezingered exposure

option located in the upper left hand corner of the data collection strategy menu.

The Exp. Time, the time set for each frame should be set so that your data set is finished in time

for the next user to get on. Typically, this will be by about 9AM. The data collection time does

not include the added time needed for detector overloads. Normally, you would set the data

collection to end a couple of hours early to allow for these overloaded images. The Rigaku

strategy is to recollect every image at one tenth the original scan time to recalculate reflections

whose intensity exceeds the linear range of the detector. For example, if the exposure time is set

to 60 seconds per frame, an overloaded image will be collected for 6 seconds. If the dezingered

option is selected, two 60 second frames will be collected for each setting of the crystal to

remove random noise, spurious radiation peaks, etc. Two 6 second overload images will also be

collected.

When you are satisfied with the data collection strategy, hit the run button and data collection

will begin.

INTEGRATION

When the data is collected, you will see the following screen.

By default, all the framesets collected will be listed under the To Use column heading. The

resolution should be set to that selected in data collection. If using d*trek, select the Advanced

tab and check the box “refine reflections and refine before integration”.

Hit run to begin integration.

At this point, you will be asked to create a mask file to exclude the beam stop shadow from the

integration area. If you do not have a mask file you should create one now.

Using the mouse and the boxes containing the square and the circle, mark out a region of the

detector encompassing the beam stop shadow.

When satisfied with the results, save the mask file using the save icon, .

You will not need a mask file when integrating using fs-process. When completed, you will be

prompted to run a Laue check, which will check the diffraction symmetry. You should already

know the Laue symmetry but this is a useful check.

Hit the run button and the results are similar to that shown below.

In the above example, the crystal had several unit cell possibilities, which are listed with

increasing symmetry. -1 is triclinic and will always be shown. There are two monoclinic

settings, one (in green) has an Rmerge of 0.06 and this is the correct Laue group. Ordinarily, the

Laue group for triclinic will be the lowest because there are fewer reflections being averaged.

You should choose the setting that yields the lowest Rmerge having the highest symmetry. For a

good crystal, an Rmerge below 0.05 is not uncommon but depending on how many reflections

are being averaged, you can see Rmerge values above 0.10 or higher.

Once you have decided upon a Laue group, you are ready to scale and average the data. At this

stage, an empirical absorption correction will be applied and a .hkl file will be generated.

The typical settings for the scale and average routine is shown below. A file, shelxl.hkl, will be

written to the data collection directory selected. After scaling the data, you will run a final least-

squares unit cell refinement and generate a cif file summarizing the data collection experiment.

The cif file is written to Crystal_Clear.cif and to filename.cif, where filename is the data crystal

name. The two files are identical.