MAR FAQ

Filters/Attenuation are displayed as the % transmission of the incident beam. Each beamline has a number of Aluminum and Tin filters that are used to attenuate the beam. The % transmission is calculated for the beamline energy and displayed – if the transmission is not 100%, then the number is displayed in red. The 2 primary sergui pages for changing the energy are the main hutch and collect single pages, shown below. To change the attenuation, enter the desired % into the entry field and hit a carriage return – note that the displayed number will be different from your entered number as the program will place the combination of filters that would most closely approximate your request.

The detector will not move?

The most probable reason that the detector is no longer responding is that one of the motors that controls the detector’s motion has gone into open loop. The easiest way to diagnose this problem is to look in the terminal window in which you started sergui, you will see an error message with the term “open loop” in it some where. To fix this problem, open a new terminal window and enter the following command: reset_mx <cr>. After you enter this command, you will see a number of commands scroll across the terminal window (the rest_mx command resets a fair number of potential control system problems). You should be able to move the detector now.

The robot will not dismount my sample?

The most prevalent reason that the robot will not dismount your sample is that there is too much ice built up on the gripper to properly grab the base of the sample. Try defrosting the gripper and then repeating your dismount command.

Is it okay for me to reboot a computer?

The answer can not be to forcefully emphasized:

IT IS NEVER OKAY TO REBOOT A COMPUTER WITHOUT EXPLICIT INSTRUCTIONS FROM THE CAT STAFF!

If you are encountering a problem where you ask yourself if you should reboot a computer, you should pick up the phone and call somebody!

My NX session is running very slow, is there anything I can do?

This problem shows itself during sample alignment. You will experience a length delay in the update of the video display on the sergui sample page, which can make the procedure very painful. Our experience has been that your home institution is limiting your available bandwidth because they believe that you are downloading music or videos off of the web. The problem has been traced to the video display on the sample page. You can try and fix this problem long term by contacting your local IT person and getting a fixed bandwidth prioritized for your local domain. The short term fix is to disable the video feeds by selecting the disable button on the camera selection section of the sample page.

Once you push the disable button the sample video will no longer update. You can monitor the sample by using the web based video display. You have a few options on how to align your sample with the video feeds disabled:

(1) Use the Auto-Align feature

(2) Use the Fine Adjustment buttons

Either of these options (or both) can be used to align your sample without an active sample video display in sergui.

I measure good diffraction at some angle of phi but not others, what can I do?

There can be a number of reasons that can cause you to have a variation in your diffraction at different phi angle, including:

(1) The sample geometry may contribute to this problem. If the sample is a plate, then you may be shooting through significantly different samples volumes. If this is the case, you can try to collect data with an appropriate phi offset to collect some frames with a similar volume.

(2) The sample may not be properly aligned to the spindle axis. Make sure that you know where the sample is and realign if necessary – sometimes it is difficult to see a small sample if there is ice in the loop. You could try aligning to parts of the loop and not pay attention to where you think the sample might be.

(3) The beam and the goni rotation axis may not be aligned. Mount and align a phosphor and follow the instructions given in the goni alignment section of this user guide.

(4) One of the most common problems is a small misalignment of the x-ray beam with the height goni rotation axis. Even if the sample is properly aligned, if the rotation axis is not at the beam height you can have problems hitting a small sample with a small beam. What can happen is that part of the sample is in the beam at 1 phi orientation, but is not in the beam at another.You can use the goniometer gui (from the setup pull down menu) to make small adjustments to the height of the goniometer. A good test would be to start at a phi with diffraction and then make small adjustments in the goni height to optimize you signal – you should choose a reflection or 2 and use the same oscillation range. Then rotate 180 degrees and repeat. If you can not get good diffraction at these 2 angles without significant changes in the beam height, then either your sample is not aligned (most probable) or the GUI red cross hairs are not correct.

(5) The red cross hairs for the sample centering may be off. Every hutch has an alignment needle located on the goniometer, which can be used for system verification. If you mount the alignment needle and find that the red cross hairs are not in the correct place, then contact your local user support and let them know, they may walk you through a protocol to recheck and then adjust the position of the cross hairs.

Missing Frames

Sometimes frame(s) are not transferred to your BM(ID)_name.raw/your_directory directory. Do not panic, the frames are on the local MAR computer and can be recovered. Sit down at the appropriate 3-panel control computer (where you run sergui from) for the missing data and open a new terminal window. In this new window enter the following command: get_frames <cr>. The frames should be moved over to the BM(ID)_name.raw/your_directory directory. If your frames are not being moved over then contact your local user support for further assistance.

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