The following is an outline procedure for collecting data on the SMART system. It presumes that you have read the help sheet "General Rules For Using the SMART System." It also contains simple warnings about how not to abuse the system or the diffractometer.
The SMART system consists of the SMART diffractometer and detector
(and their controlling computer interfaces) and the SMART program
running on the Pentium-II in Room 32A Lewis. The APEX system consists
of
the APEX diffractometer and detector and the SMART software running on
the Pentium-4 in room 32A Lewis. Operation of both systems is
essentially identical. For differences in the use of the APEX
system, please read this document.
Operations in the program will affect the diffractometer and detector, and the diffractometer and detector will affect the program. Try not to damage either.
Get your crystals ready to mount and examine them optically to make sure that they are reasonable. Check out an XYZ goniometer head (be sure to fill in the card) and make sure that it is equipped with the long pointed brass pin with a suitable quartz capillary mounted on it.
DO NOT USE GONIOMETER HEADS WITH ARCS!
DO NOT USE A SHORT PIN!
IF YOU DO SO, YOU WILL DAMAGE THE DIFFRACTOMETER!
Sign the log-book and follow the procedures to set up your subdirectory as outlined in the help sheet "General Outline of Data Collection on the SMART System". Start smart from the DOS prompt by typing smart. This will cause the blue-screen to disappear and a window to open on the WinNT desktop. You will see two blocks, [Command Prompt - smart] and [SMART: Bruker Molecular...], on the taskbar at the bottom of the screen. (If you see more than that, then someone has left sessions open. You may want to investigate them and close them if it looks reasonable to do so.
A subwindow will open which says "Last Project was in <name>.
Return to this project?" Click on [No]. The next subwindow will
say:
"Return to another, pre-existing, project?" Again, click on [No].
The next window will be "Configure Options" (a much larger window). However, the only entry you need to make will be the one for Crystal Name. This should be a word which can be used as a file-name. Alphanumeric characters only, no special characters and NO BLANKS. (Although it is not necessary, we recommend that it be identical to your <mydir> directory name.) Only the crystal name needs to be entered. (This will also be the "project name".) The program will automatically run in the subdirectory you started from and put all your files there.
The program will now show you the "Project Defaults" window. Click to highlight Small Molecule and click [OK].
Pull down (<LMB>) Goniom.
In the Goniom pulldown, select Generator.
In the dialog box, make sure that the KV are set to 50 and the mA are set to 30.
<Enter> will activate the settings and return you to the window.
In the Goniom pulldown select Optical. [Keyboard shortcut: hit <CTRL/O> from the main window.]
The system will display a dialog box. Ignore it and hit <Enter>.
The manual control box is now active. The goniometer should be in position with the Phi Block swung around near the front and the detector swung away by some amount. Pick up the crystal on the quartz capillary with the slime and mount the goniometer head on the base and tighten it. (Once the crystal is centered (as below), you might want to check to see if the crystal is in the center of the low-temperature stream, using the mirror. The throat of the nozzle should appear as a circle in the mirror and the crystal should be approximately centered in it. Do not move the low temperature apparatus more than a small amount, very carefully, if the crystal is not in the stream. If it is only slightly off-center, leave it alone.)
Please note: The SMART system will take data on small crystals. In order to assure beam uniformity for the crystal, the absolute maximum dimension of your crystal should be less than 0.50 mm. That means the diagonal of a cubic crystal, for instance, not the edge. A good size for a crystal is about 0.15 x 0.15 x 0.15 mm but smaller is usually OK.
Use the manual control box and adjust the sledges and height adjustment on the goniometer head to bring the crystal to the center of the diffractometer. The manual control box has four buttons labeled A,B,C,D. It has a button in its upper left quadrant labeled "Axis Print", and "GO". (This is the same manual controller that Bruker uses on other instruments, which is why there are a bunch of other buttons and labels, too. Ignore them.)
With one of the four buttons depressed, pressing <GO> will cause the goniometer to drive to a specified position. C and D specify positions with the Phi Block near the front, A and B with the Phi Block near the back, both positions have the Phi axis perpendicular to the line of sight of the microscope/telescope. The Phi angles of the two buttons are 90o apart. Pressing the <GO> button a second time will cause Phi to rotate by 180o, thus allowing for convenient centering of the crystal. There is a light on a flexible extension which can be positioned to illuminate the crystal. Please pull it back away from the crystal before switching from the C,D to the A,B position. You should be able to center the crystal to within less than one of the small divisions of the scale in the telescope. Adjust the left-right centering in the C,D positions, and adjust the height in the A,B positions. This last is a bit tricky, since the cross-hairs will no longer be aligned with the spindle.
As of this writing, the center of the diffractometer is near the
center of the crosshairs on the telescope. However, this is not a fixed
point, nor should you count on it.
DO NOT "ADJUST" THE TELESCOPE, EITHER TO "FOCUS" IT OR TO "FIX" IT!
IF YOU REALLY THINK IT IS OUT OF ADJUSTMENT, ASK DR. HOLLANDER OR DR. OLIVER TO FIX IT!
REPEAT -- DO NOT ADJUST THE TELESCOPE!
Now go to Step 4.
If you are using the APEX system and are centering your sample,
there are several differences between the APEX system and the SMART
system.
Sample mounting and initialization of the program to get it the
state where you are ready to center the crystal are the same as for the
SMART diffractometer. the only differnce
being that the keyboard short-cut to enter the optical mode is: <CTRL/SHIFT/O>.
When your sample is mounted on the goniostat and is in position to
center, turn on the illuminating lamp. You will also need to open
the Video Display on the PC. Double-click on the "video" icon on the desktop. A
window will open with a feed from the optical camera mounted on the
instrument. Your crystal should be visible within this window.
Unlike the SMART controller, you do not need to press "Axis Print/GO" to drive the axis. Simply
pressing the A, B, C
or D button will drive the
axes.
Adjust the crystal position in the same manner
as you would for the SMART instrument (see above). Again, you
should try to adjust the position of the crystal such that it is as
close to the center of rotation as possible. Left/Right
adjustment
of the crystal positoin can be achieved at the "C" and "D" positions, while the "A" and "B" positions allow you to adjust the
height of the crystal. As with the SMART system, the center of
rotation is near the center of the cross-hairs, but is not on them.
Once your crystal is centered, drive to either the A or B
position, and then use the <esc> key to get control back
to
the SMART window. (Note that in this case you cannot use the <RMB>;
it doesn't work.)
DO NOT "ADJUST" THE TELESCOPE, EITHER TO "FOCUS" IT OR TO "FIX" IT!
IF YOU REALLY THINK IT IS OUT OF ADJUSTMENT, ASK DR. HOLLANDER OR DR. OLIVER TO FIX IT!
REPEAT -- DO NOT ADJUST THE TELESCOPE!
Select Detector
Select Dark Current
The dialogue box should show a time of 10 seconds and a filename of .\dark10._dk. Hit <CR> to accept these values.
The system will now take 16 10-second frames without opening the shutter and average them to get the signal generated by the detector when there are no X-rays hitting it. You will only need to do this one time per data set for each set of counting times. At the end of this procedure the display area will show the dark current frame in uniform bright yellow. (If it is not uniform, call Dr. Hollander or Dr. Oliver; there is a fault.)
NOTE: The current SMART CCD detector has a bright/dark spot
in
the lower right corner and isn't nearly as uniform as one might expect.
This is normal for this particular detector. When the view of the dark
frame is displayed, control has returned to the SMART window.
NOTE: The APEX instrument will not display the dark frame. The
screen will be apparently blank. This is normal for this
instrument. The dark frame will be resident when you start your
unit cell and data collection. If you wish to feel secure that
the dark frame is indeed resident, select the Detector menu, followed by Load Dark. Make sure that the
filename matches (dark10._dk
for example) and click on OK.
Pull down the Crystal menu.
<LMB> on Unit Cell
Hit <CR> to accept the default values for the Matrix Scans.
[Keyboard shortcut: <alt/C>, U, <cr>. ]
The system will now collect three sets of 20 scans, each 0.3o wide in omega and measured for 10 seconds. It will display each frame in the display area immediately after taking it. This allows you to immediately check for a bad crystal. If the crystal is bad you can hit <esc> and wait for the end of the current frame, then go back to step 3).
After collecting the 60 frame set (about 15 minutes), the Matrix routine will scan the frames for spots, put them into a list and attempt to discover a reduced primitive reciprocal cell, index the reflections and determine the orientation matrix and cell dimensions. It will flash up various screens as it is doing so, finally coming to rest in one which shows cell dimensions. Look over the output shown and evaluate it. You then want to include all the reflections in the array.
Hit <Enter> to get back to the main window.
Select Crystal pulldown.
Select Modify. [Keyboard shortcut: <alt/C>, M ]
In the dialog box check the last line. It should say "+CH" or
"+CH".
If so, hit <CR>. Otherwise set it to +CH and press <CR>
The screen will show the list of reflections. Press <CR> to get back to the window.
Select Crystal pulldown.
Select LS
In the dialogue box pull down (<LMB>) on the Constraint box and select -1 Triclinic. Either <LMB> on the [OK] button or simply press <Enter>.
If the information line at the bottom of the window says that one or more reflections are being rejected, hit <Enter>. You will want to investigate the matter, however.
The program will now do a non-linear least-squares refinement (unconstrained by symmetry) of the cell dimensions and other parameters against the positions of the reflections measured from the frames. It will then display an output which includes the parameters, their e.s.d.'s, a series of histograms of errors in H, K, L, omega, X and Y, a list of the reflections with the worst deviations and the complete reflection list. This output can be paged through with the arrow and page keys and should be examined to determine if the crystal is worthy.
Get back to the main window by pressing <CR>. If this is not the first time you have run LS, then you will also have to hit <Enter> to update the files.
If the crystal appears good, and you have higher symmetry than triclinic, you want to go back into LS and refine with a flag of -n (where the appropriate value of n can be selected from the Constraint Box) to get a constrained refinement. Be sure to check the goodness of fit parameter for the constrained refinement and compare it to that for the unconstrained refinement. It should always be a little worse, but not drastically so.
We always collect a hemisphere of data. The variables which may be altered are the X-ray generator settings and the exposure time per frame.
IF YOU HAVE A TRICLINIC CELL then you want to collect some extra frames to increase redundancy for the empirical absorption correction. How to do this is given below in the same section as how to change the exposure time.
Maximum settings for the generator, without special permission, are 50KV and 48mA.
Minimum time per frame is 10 seconds. At ten seconds per frame, data collection takes a little more than 6 hours. At 20 sec. per frame, about 10 hours. At 30 sec. per frame, about 14 hours. The APEX takes 1-2 hours less per dataset. How much time you spend per frame is dependent on your crystal scattering intensity. You want to have significant intensity near 45 deg., but you don't want to overload the detector too often with intense low-angle spots. You also want to be courteous to other users who might be wanting to use the system, so don't spend more time than you really have to. If you are collecting extra frames for a triclinic cell, increase the quoted collection times by 15 percent.
If you are going to use a counting rate of 10 seconds per frame skip to step 7).
If you are going to use a longer counting time, you need to collect a new dark frame.
Select the Detector pulldown.
In the pulldown select Dark Current.
In the dialogue box, enter the number of seconds on the first line. On the last line, change the last two digits of the filename to correspond to the number of seconds. i.e., if you are using 15 second scans changed the filename to .\dark15._dk. While not strictly necessary, it does keep your ten-second file from being over-written, and serves as a reminder of the data collection parameters.
<Enter> will cause the system to measure the new dark current frame and set it for current use in frame collection.
Select Acquire pulldown menu
Select EditHemi.
At the end of each line, change the scan time from 10.00 to your selected time.
IF your cell is TRICLINIC change the last line so that the Phi vlaue is 55.0 and the #Frames value is 230. (Other values may be substituted once you fully understand the operation of the machine. This is a set which works reasonably well.
Hit <CR> to save your result and return to the window.
Select Hemisphere. [Keyboard Shortcut: <alt/A>, H , or F2 ]
A dialogue box will appear. On the first line enter the base filename which will determine the filenames of the stored frames. (This should be seven characters or fewer, all alphanumeric, no special characters and no spaces.) If you enter, for instance, ringo, then the frame filenames will be generated by the program as ringo0.001 through ringo0.606 then ringo1.001, etc. for the four sets of scans. On the second line, enter any informative title you wish. This will appear in the file headers for the scans, and also on the screen during data collection. It is recommended that this name be related to your mydir name, just for consistency, but it can be anything. For compatability with the case-sensitive Linux system, it is recommended that you use lower case letters when forming the filename.
Do not change any of the remaining lines unless you really know what you are doing. (Trust me -- you don't know what you are doing.)
The system will now collect data. At the end of data collection, in six, ten or fourteen hours or so, a window will appear, saying No more runs in EditRuns array. This is the normal exit.
Hit <Return> to get back to the window.
Select Goniom pulldown
Select Optical.
On the manual control box, depress A or B, then <GO>.
Now depress D and <GO>. This procedure gets you back to the normal starting position faster than just depressing D and <GO>. It has to do with the fact that the detector has to move as well and the system keeps omega from moving rapidly if the detector is moving.
Hit <esc> to get back to the window.
Select Goniom pulldown
Select Generator.
Make sure the values are 50 KV and 30 mA.
Hit <CR> to get back to the main window.
Select File pulldown. Select Exit. Press <Enter> to confirm the exit. Press <Enter> to confirm the default selection of smart.ini as the configuration file and and to over-write it with the current values of your parameters. This returns you to the desktop. Click on the taskbar block which says [Command Prompt] to return to the bluescreen for transfer of data.
Remove your goniometer head and crystal and transfer your data as
given in the help sheet General Outline of
Data Collection on the SMART System.