***IF AT ANYTIME YOU DO NOT KNOW WHAT TO DO OR SOMETHING DOES NOT LOOK RIGHT, CONSULT A CRYSTALLOGRAPHER***

If it is after hours, call Danielle (login to see number):

1. Checking the liquid nitrogen and starting a new project:
   1. Make sure the Cryostream is off before beginning your experiment
      1. Behind the instrument, look at the blue Cryostream Controller box: 
         1. The top TEMP display tells the current temperature, while the bottom STATUS display tells the current status of the Cryostream.
            1. If the TEMP display says SHUTDOWN, the Cryostream is currently off. Continue to Step 2.
            2. If the TEMP display is showing a temperature, you need to turn off the Cryostream:
               1. Press the red STOP button once. The TEMP display should switch to SHUTDOWN. Continue to Step 2.
   2. The APEX3 software should be open. If it is not, open it from the desktop (do not open APEX3 server software).
   3. Click the Sample dropdown in the top left of the screen and select New.
      1. In the New Sample Window:
         1. Name = MCL Project Number (insert a "d" between the first letter and number and "p" after the last letter)
         2. Group = Users
         3. Folder = Same as the "Name." Make sure there is ' \ ' between the drive and folder name (if the box is pink, something is wrong).
         4. Click OK.
   4. ALWAYS SAVE THE CURRENT PROJECT IF YOU ARE ASKED, THAT IS SOMEONE ELSE'S DATA.
2. Once you have set up your new project:
   1. Click the Setup tab on the left and select "Describe"
      1. Fill in the empty boxes:
         1. Compound: project name_user's sample ID from lab notebook_user's name/advisor's last name (Example: bd83bp JAB58 Jeff Bertke/Gray)
         2. Formula: anticipated chemical formula.
         3. ***NOTE: NO RINGS, WATCHES, BRACELETS, ETC., MAY BE WORN WHILE YOUR HANDS ARE INSIDE THE INSTRUMENT. THESE ITEMS CAN SCRATCH THE FACE OF THE DETECTOR.***
   2. Configuring the Instrument and Centering your crystal:
      1. Click Center Crystal in the Setup tab
         1. Click the Mount button in the bottom right corner, once the goniometer stops moving, you can open the doors. To unlock the doors, press the circular silver buttons at the end of each black handle and slide the doors apart.
         2. The beam stop for the Mo source must be removed and replaced with the correct placeholder. These pieces are held in place by magnets.
            1. Carefully remove the Mo beam stop (the one in back) and set it aside.
            2. Find the Mo beam stop placeholder, and carefully put it in place. The two small gold prongs on the instrument will match up with the two small gold circles on the back of placeholder when installed correctly.
         3. Close the doors by sliding them together until you see the lights inside the enclosure dim.
         4. Click the Center button in the bottom right corner. Once the goniometer stops moving, you can open the doors and mount your sample.
         5. Use the tool to center your sample in the crosshairs on the screen. Only adjust from the front of of the goniometer to center the sample.
         6. Center your sample with a series of 180 degree and 90 degree rotations using the large buttons on the computer inside the enclosure. ONLY CLICK THE SPIN PHI 90/180 BUTTONS. If you try to move any axis other than phi with the doors open, it will result in an instrument error. 
         7. Once your sample is centered, place the tool inside the enclosure and close the doors by sliding them together until you see the lights inside the enclosure dim. 
3. Collecting Data
   1. Click on the Collect tab on the left.
      1. Click the Experiment button on the left.
         1. Click the Load Table button at the bottom of the screen. A window will pop up. Click the button to go up one folder and then select pxrd_photo2.exp. The experiment will load.
         2. Click the Validate button on the bottom
         3. If all operations are valid, click the Execute button and your experiment will begin. 
   2. Collecting a set of correlated frames
      1. After the experiment from 1.A.iii is running, change the name of your sample to the filename or prefix box from "filename" to "filename1".
      2. Click the Execute button again. You will get a warning message that an experiment is already running and the second experiment might overwrite data from the first experiment. Acknowledge this message so that the second experiment will run as soon as the first one is completed.
   3. Generating the set of correlated frames
      1. After both data collections have been completed, open a command line in the folder containing your data.
      2. Use the following command to execute the correlation script: bnrun C:\bn\correlate.pyc filename_*.sfrm filename1_*.sfrm
      3. After a short while, your working folder will contain a set of files named "correlated_filename_*.sfrm".
4. Integration and Creating a .raw File
   1. Click on the Reduce Data tab on the left and select Integrate Debye Rings.
      1. Click on the folder at the top of the screen and in the pop-up window. 
         1. Navigate to your project folder.
         2. Highlight all of the correlated_filename_*.sfrm files and click Open.
      2. All of your individual collected frames will load and merge into one image on the screen. To integrate your data:
         1. Click on the pac-man shaped icon at the top of the screen.
         2. In the red area, click and drag to draw a box. 
         3. In the boxes below, type in the minimum and maximum 2 theta you want for your powder pattern. (2-theta min = 5; 2-theta max = 60, 80, or 100 depending on how far out the sample diffracted). 
         4. Changing the value in the Region Height box will vary the size of the wedge being integrated. Generally, you'll want to integrate the largest wedge that gives your a nice pattern.
         5. Right click in the red area and select Integrate to integrate the wedge you have defined.
         6. The powder pattern will appear at the bottom of the screen. Look closely at the pattern to make sure there are no unnatural sudden changes in intensity.
            1. If everything looks good, right click in the red area and click Create Raw File. Save the raw file in your project folder.
            2. If there is a problem; lower the value in the Region Height box, right click to integrate again and see if the problem went away. Repeat this until there are no sudden changes in intensity. If the problems persist, you might need to recollect the data with new dark images. At this point, consult a crystallographer.
      3. Saving the raw file is the final step. If you have another sample to collect, create a new project as described previously in Step 2 of the first section. 
      4. If you have no more samples to collect, you need to return the instrument to its original configuration:
         1. Move the instrument to the Top position, remove the Mo beam stop placeholder and install the Mo beam stop. Refer to Step 2 of the second section.
         2. Once the beam stop has been installed, close the doors and click the Center button to move the goniometer to the center position.

NOTE: THE TOPAS SOFTWARE PROVIDED ON THE MICROSCOPE COMPUTER CAN BE USED TO OPEN YOUR .RAW FILE AND CONVERT IT TO A MORE USEFUL .XY FILE.