Collecting X-ray Crystallographic Data at Home Source


2004-04-13 – Gour Pal


Our X-ray facility includes mar300 image plate, Rigaku X-ray generator operated at 50 kV and 100 mA; which is equipped with Osmic mirror and oxford cryosystems for cyo-cooling. To maintain this facility, it further includes a chiller- a cooling device for the x-ray generator; He-gas supply to keep the Osmic mirror clean constantly during data collection, Dry Air Unit to supply dry air for cryo-cooling, an UPS system to prevent any undesired interruption of data collection due to voltage fluctuation or power interruption and Dewers filled with liquid nitrogen.


Anybody intended to collect data using this facility should be aware of the following items in the very first place:


1.                  X-ray generator is on full power: Usually, if there is no user, we lower the operating power of the generator at 20kV and 10 mA. If it is not in full power start to increase the power slowly with each step of 2kV and 6 mA and includes a pause of 1-2 mins. after each step. Please allow longer intervals of 5-10 mins. at the points of 30 kV and 40 kV. If the filament is new double the time lag and be very slow higher than 40 kV and do not go for full power on the same day when filament has been changed. Maximum recommended power  is 46 kV and 90 mA on the first day. This aging usually takes an overnight but sometimes it may take about 3-5 days. Remember, while yor are increasing the power of the generator, at any point your mA should not be more than the double the value of kV. For example, 36 kV and 72 mA is okay but NOT 36 kV and 74 mA.

2.                  There is enough liquid nitrogen in the Dewer for running the cryo atleast for overnight- if you want to use the cryo device. For a rough estimate, a full Dewer of 50 L capacity (white elongated one) can run the cryo continuously atleast for 60 hrs. (three nights and two days).

3.                  Dry Air Unit is running. If there are successive users, usually we do not turn off this unit. However, once it is switched OFF, it needs to run atleast overnight prior to your experiment after you switch it ON. Please plan accordingly.While you turn ON the dry air unit, check the flow of the air in the flowmeter attached to it. Flow should be 10 L/min.

4.                  Next useful item is He-gas. Please check there is He-gas in the tank. Pressure-gauze on the valve will indicate the gas pressure as soon as you turn the knob. If there is no gas pressure inform G.Pal (or in his absence Qilu Ye or Jim Blond) who can arrange for a new tank.


Once all of the above conditions are satisfactory, you can turn the cryocontroller ON, set up your desired temperature (usually 100 K) on PROGRAM Screen and START. Normally it takes 1-2 hrs depending upon the RAMP you selected. If you are a first time user, ask any senior member of the lab to demonstrate you this step. [When you finish the experiments go to the same PROGRAM mode RAMP up the temperature to room temperature and END the task with the same START button].


After the cryocontroller indicates that it has reached the desired temperature and you have brought up the X-ray generator to its full operating power of 50 kV and 100 mA, turn ON the He-gas and adjust the gas pressure on the valve. Limit of the gas pressure indicated with a BLACK mark on the meter which is located on the top corner of the X-ray enclosure.


Now you are ready to mount your crystal on the loop or capillary for the X-ray experiments.


BE CAREFUL! IF YOU WANT TO OPEN THE X-RAY ENCLOSURE FOR MOUNTING CRYSTAL ON THE MACHINE, PRESS THE RED BUTTON ON THE SIDE PANEL OF THE GENERATOR. Yellow light will be flashing with a periodic sound. Under this condition there will be no x-ray even if the main shutter of the generator is ON.


Once you are satisfied with the mounting and alignment of the crystal, close the enclosure very carefully up to  the mark as indicated and switch ON the main beam shutter of the x-ray beam. If it is already ON (it may happen if you forget to switch it off before opening the enclosure) then turn it OFF and then turn ON again- otherwise there will be NO X-RAY BEAM. And it will be indicated with a ERROR MESSAGE as soon as you start data collection that “X-ray intensity is too low”.


LOGIN in the computer and create your own directory where you intend to collect your data and then type “mar”. It will pop up your data collection window where you can adjust the distance between the crystal and the image plate, set the starting oscillation angle, oscillation step, effective diameter of the image plate etc. And START data collection- if you are sure you have put your name in the log-book beside the computer. For the image plate distance, DO NOT go closer than 100 mm or more than 400 mm. During your data collection if you experience any problem or if there is any pop-up “Error Message”, please note down details in the log-book and inform Dr. G. Pal (or in his absence Dr. Z. Jia). For your X-ray data collection further manipulation namely slit adjustments are required. In the absence of any prior demonstration to you, Please ask any senior member to assist you if you are a new user.


If you experience any other problem not mentioned above or if you find difficulties to follow this protocol, please ask Dr. G. Pal or Dr. Z. Jia. PLEASE DO NOT OVERDO ANY OPERATION.


Once you finish the data collection, please make the x-ray room tidy enough and hand over the machine to the next user if there is any on the queue. If there is no other user after you, systematically turn off all the facilities.  For example:  1. logout from the computer; 2. close the main shutter of the generator; 3. remove the crystal from the machine and store that properly. 4. if you do not want to store the crystal then wash the loop properly and store it ;5. lower the power of the generator to 20kV and 10 mA in the same manner as you increased the power i.e. by the steps of 2kV and 6mA. 6. close He-gas; 7. set the cryocontroller to room temperature and  start END task.8. once the crycontroller indicates that it has reached room temperature, switch it OFF 8. and switch OFF the dry air unit