These instructions pertain primarily to using a SMART CCD area detector with the Bruker P4 diffractometer that is available at the University of Wisconsin, Chemistry Department.

1. Log into the NT computer (P32) next to the instrument using the xtal account on the chmxray domain.
2. Start the SMART program on the PC (Start, Programs, Bruker-AXS Programs, SMART). When the program asks if the angles are at 0 degrees always say yes, even if the angles are not at 0.
3. Set up the project information for this sample in Crystal/New Project. Both the working and data directories should point to the same directory and should be on the s:\ device. Be sure to include the chemical formula, crystal description, and data collection temperature.
4. Optically align the sample using the Goniometer/Optical option. Drive all axes to zero when done using Goniometer/Zero.
5. Take a rotation frame image of the crystal using the Acquire/Rotation option. If the rotation frame shows no spots or if it shows powder diffraction rings, mount and align another crystal.
6. Determine initial cell parameters with the following series commands.
• Acquire/Quadrant with default parameters will record two series of frames (~ 20 minutes). Set the Job name to "matrix". The default series of frames are the following:

   
  #  2Theta Omega Phi Chi Axis Range   # Time
  0    30     30    0  40   3   0.4   30  10
  1    30     30   90  40   3   0.4   30  10
     

• Crystal/Redtn Cell will threshhold the frames, pick spots, index spots, test for possible higher metric symmetry, and refine the cell parameters. You should see one or more lines of "1"s in the indexing step. If the program finds very few (< 20) spots or indexes only with an implausibly large unit cell, try another crystal. If the program has trouble indexing the spots or refining the cell parameters and you feel this is otherwise a good crystal, collect triclinic data and try the twinning programs.
• Crystal/Modify will use all located spots.
• In Crystal/L S reset the omega and chi zero angles to "0.0". Initially set the maximum deviation RLV (Reciprocal Lattice Vector) to 0.05. In subsequent refinements, use smaller values for the RLV deviations in order to remove any large outliers. Refinement is complete when the largest RLV deviation is < 0.03 and the largest omega deviation is < 0.2. For the final cycle of refinement, run Crystal/L S with the crystal system set to "-1".
7. Test the validity of the unit cell.
• Check the fit of the spots to the unit cell with Analyze/Display. Be sure to turn on the calculation of hkl locations. Examine several frames to confirm that the cell does properly fit the peak postions.
• Estimate the volume of the molecule (18 * # of nonhydrogen atoms). The estimated volume should be an integer multiple of the cell volume.
• Test to see if the structure has been previously determined by checking the Crystal Data File Database. This check is performed by the Crystal/CDF Search routine.
8. Optimize the scan runs using the ASTRO program or use one of the following sets of runs.

   For triclinic symmetry use the following runs. Note these are already set up in the Acquire/EditHemi. Depending on the scattering ability of your sample, you may want to change the count time.

    
      #  2Theta Omega Phi Chi Axis Range   #   Time
      1    30     30    0  40   3   0.4   910   20
      2    30     30    0  15   3   0.4   910   20
      3    30     -5    0 330   2   0.4   105   20
      4    30     -5   90 330   2   0.4   105   20
      5    30     -5  180 330   2   0.4   105   20
      6    30     -5  270 330   2   0.4   105   20
      7    30     30    0  40   3   0.4    50   20
          

   For higher symmetry samples the following series of runs usually proves adequate. These runs are already entered in the Acquire/EditMulti set.

    
      #  2Theta Omega Phi Chi Axis Range   #   Time
      1    30     30    0  40   3   0.4   910   30
      2    30     30    0  40   3   0.4    50   30
          

   If greater redundancy is needed, add more phi scans at different chi values(with our 30 deg offset low temperature nozzle, chi must stay in the range -35 to +60 degrees). For weakly diffracting samples, increase the count times up to a maximum of 120 sec/frame.
9. Select the proper dark current for the desired scan time in the Detector/Dark Current/Load Dark menu. The last three digits of the dark current file names give the count times in seconds used to collect the dark current data. If you can find no dark current file for your count time or if you want to collect a newer dark current correction, then go to the Detector/Dark Current menu and select the desired Seconds per exposure and file name (F404L###._dk).
10. Start data collection using either the Acquire/Hemisphere or Acquire/MultiRun command. Be sure to set the Job Name to the name being used for the project. Do not change any other options except the Job Name or the Title.
11. After data collection has completed, start the data integration program SAINT Plus (Start, Programs, Bruker-AXS Programs, SaintPLUS).
12. Set up project description by selecting New under the Project menu. Enter the project name and indicate the location of the data frames by selecting the .p4p file corresponding to the first set of data runs.
13. Two additional steps are needed before starting SAINT. In the SAINT menu, first select "Initialize". Then under the SAINT menu select "Execute". In this display change the "Crystal system constraint for integration(K1)" to "Triclinic". Check the Bravais lattice type listed in the lower right corner of the screen. Begin SAINT by selecting "Integrate, Sort, Global" button from the SAINT menu.
14. When the integration is complete, clean up the files with the following Command Prompt command: clean newdir
15. Log out of the xtal account on P32. Log onto one of the other NT computers in your own account and copy the s:/newdir/newdir.* files to your directory. If the S: device is not defined in your account, open Explorer (Start, Programs, Windows NT Explorer), open the Map Network Drive icon, Select the drive letter S: and map S: to the frames4 share on the P32 computer in the CHEMXRAY domain.

1. Filling the Small Dewar From the Large Dewar.

The small Dewar on P32 needs to be filled at least once per day. The Dewar connected to P51 needs to be filled at least twice per day (suggest morning and evening).

Each large Dewar should have an adjustable wrench and a canvas glove. The glove should be used as a "hot pad" to insulate your hand from the very cold metal valves and pipes.

1. Connecting Dewars. Thread the brass fitting on the flexible metal hose from the small Dewar to the "liquid" port of the large Dewar by hand. Finish tightening the brass fitting with the adjustable wrench.

2. Filling the small Dewar. Open the valve on the "liquid" port of the large Dewar until a pulsing sound is heard. After about 1-2 minutes the pulsing sound should stop. Now open the valve on the "liquid" port all the way open using the cloth glove. Once the valve is opened, place the glove on top of the blue level indicator on the large Dewar.

   Note that the small Dewars typically take about 10-20 minutes to fill. Do not leave the room when filling the small Dewars, or it is likely that the small Dewar will overflow and the entire contents of the large Dewar will empty onto the floor.

3. Slow filling. If nitrogen is flowing slowly from the large Dewar, as often happens after the large Dewar has been filled, then open the "Pressure Building" valve on top of the large Dewar two full turns.

4. Whistling sound. If you hear a whistling sound coming from the large Dewar, then the large Dewar is empty. Close all valves on top of the large Dewar using the cloth glove, and refill according to the instructions below.

5. Completing the fill. When the small Dewar is full, close the valve on the "liquid" port of the large Dewar using the cloth glove. If the "Pressure Building" valve was opened during the fill, be sure to close this valve also. Each day record the group or groups to be charged for the nitrogen and the date on the log sheet attached to the Dewar.

2. Filling the Large Dewar.

The large Dewars have a float-type indicator, which is covered in blue plastic, that shows the approximate level of liquid nitrogen in the tank. When this marker is at the bottom, or when a whistling sound is heard during a fill of the small Dewar, then the large Dewar needs to be refilled.

1. Disconnect from the small Dewar. Close all valves on top of the large Dewar using the cloth glove. Use the wrench to loosen and disconnect the flexible hose at the "liquid" port of the large Dewar. On the P51 instrument place the end of the hose on the support attached to the instrument shell.

2. Connect the large Dewar to the filling station.

   1. Pull the large Dewar to the filling station located in room B371B.
   2. Connect the "vent" port to the flexible hose on the right side of the duct work by hand.
   3. Connect the "liquid" port to the flexible hose on the left side of the duct work by hand.
   4. Using the wrench, tighten only the tubing connected to the "liquid" port.
   5. Open the "liquid" valve and the manual valve on the manifold next to the "liquid" port connection.
   6. Set the timer on the wall for 25 minutes and push the red button.
   7. Open the "vent" valve of the large Dewar.

3. Record the nitrogen used. Divide the number of days that the large Dewar was used into 160 liters. Record the group name and proportionate amounts of liquid nitrogen used on the log sheet located to the left of the timer. Record the "student" simply as "x-ray". Place a tick mark on the log sheet attached to the Dewar to indicate when the Dewar was filled.

4. Completing the fill.

   1. When the large Dewar is full, if the timer arrow is not reset to the 25 minutes, turn the arrow counter-clock wise until the timer stops and resets itself to 25 minutes.
   2. Close all manual valves on the Dewar using the cloth glove.
   3. Close the manual valve on the manifold that was attached to the "liquid" line.
   4. Using the wrench disconnect the two flexible hoses from the large Dewar. Use the cloth glove to support the flexible hoses while disconnecting. Note, if the fittings are frozen to the short pipes, then use the heat gun located to the right of the flexible hoses to thaw out the frozen fittings.
   5. Place the glove on top of the blue plastic indicator, and place the wrench on top of the large Dewar.
   6. Return the large Dewar to the instrument room. Be sure to relock any doors that were unlocked when taking the Dewar to be filled.