Advanced Photon Source at Argonne National Laboratory   APS USAXS instrument
USAXS instrument at the Advanced Photon Source,
X-ray science division, beamline 9ID-C

Advanced Photon Source

A U.S. Department of Energy, Office of Science,
Office of Basic Energy Sciences national synchrotron x-ray research facility

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Important Commands
Recovery from MEDM crash
Routine Operations

USAXS Imaging alignment

Ultra-Small-Angle X-ray Scattering Facility

e-mail:, instrument scientist: Jan Ilavsky, 630-252-0866, and Ivan Kuzmenko, 630-252-0327,

USAXS Operating Manual

Jan Ilavsky, July 2006

This operation manual is prepared for users of USAXS instrument at APS sector 32.

Duto to current changes, this manual is likely obsolete. It will be updated when possible.

This manual is maintained by Jan Ilavsky . This document contains information intended only for operation of the USAXS/SBUSAXS instrument.

If you need help

For help with questions related to running USAXS instrument and use of Indra 2 (USAXS data reduction software), please contact the instrument scientist (Pete Jemian). With questions or problems related to the operation of beamline contact him or any UNICAT staff member.

Contact information:

Contact information
Jan Ilavsky work: 2-0866
32ID staff check poster on the doors of the hutch

Brief review of important commands

1. Change into radiography mode: useModeRadiography

2. Change into USAXS mode: useModeUSAXS

3. Tune DCM energy: tune_dcmth

4. To open/close filter shutter: openTiFilterShutter & closeTiFilterShutter

5. Start USAXS data collection: modify usaxs.mac (sbusaxs.mac for SBUSAXS) appropriately and qdo usaxs.mac (qdo sbusaxs.mac for SBUSAXS).

6. To cancel current running experiment: [ctrl]-[c] in the command line (for either USAXS & SBUSAXS) and then wait for the command line to come back before any operation of instrument.

7. To recreate all common USAXS windows, type in the unix (not spec!!) command line usaxs_windows.csh This recreates about 10 common windows used to control USAXS.

Recovery from MEDM crash

Some of the control windows we use are created using program “medm”, which seems to crash after about 24 hours when used on PC workstations with X-win32 X-windows emulator. The medm windows become unresponsive and it is impossible to create new medm windows, parts of the medm windows disappear etc. In this case user needs to restart medm. While there are various ways to do this, the least complicated seems to be following:

1. right click on the little X-Win32 icon in lower right window and select close . This will kill all X-window screens (not the SSH sessions controlling the instrument). You will lose the USAXS plot at this point, it will be recreated later on.

2. Now restart X-win 32 by clicking on its icon in the fast start button: .

3. And now go to one of the SSH sessions NOT running the spec and type: usaxs_windows.csh. This will recreate usual windows needed for USAXS control, including the USAXS plot. The data shown in previous plot are of course lost.

This can be done even while spec is collecting data. Side effect of this procedure may be, that spec may lose the standard plot used to show scanning. This plot will be eventually recreated by the usaxs macros. Also it is not necessary for instrument control…

Routine Operations

Routine operations of USAXS instrument can be divided into following few steps:

  1. Installing sample holder
  2. Surveying samples to find positions
  3. Preparation of command file
  4. Tuning beamline: USAXS or SBUSAXS
  5. Running USAXS

Installing sample holder

Sample holder installation is the most dangerous part of the process, please be VERY careful when doing this work. WORK VERY CAREFULLY, THAT YOU DO NOT BUMP THE CRYSTALS OR ION CHAMBER. Exact steps vary depending on the sample holder which is used at the time of your experiment, so detailed steps cannot be written here. Sample changing should be part of instruction before each experiment.

Often it is helpful to move sample SX position to –20 mm or so. If appropriate, use this control window. If the window is missing, please refer to the section Recovery from Various Problems on process how to get this window.

Surveying samples to find positions - Radiography

In this step user identifies positions of samples so these can be measured using the command file.

  1. Check, that the hutch is closed and properly buttoned up (all green lights – or all except the last one on the right) - on the panel next to the doors.
  2. In the command line window with fourc program type: useModeRadiography and push [enter]. Start the Photonic Science camera amplifier as instructed. This sets USAXS instrument into radiography mode.
  3. If you do not see image on the screen, check, that the TV control switches are turned properly: left to D and right to input connected to Photonic science camera amplifier (usually D also).
  4. Use SX and SY to locate your samples, locate following motor control screens: and . Procedure to pre-measure these positions should be explained to you previously. At this point list of sample names and positions in Excel is VERY helpful. Correct this list as necessary.
  5. When done, type in command prompt useModeUSAXS and push enter. This moves instrument back to USAXS mode.

Preparation of command file

Command file usaxs.mac (sbusaxs.mac for SBUSAXS) is usually used for running the instrument. There are two areas of this command file:


Top area is where geometry of the instrument is defined. User usually does not change anything here. Except, when changing between different sample holders, you will be instructed which parameters to change – generally the SDD and SAD need to be modified. Do not forget to do so.


Second area is list of samples. They are measured in the order from top to bottom. You can copy the list from radiography here. However, when copying from Excel, remove the tabs and replace them by spaces, Spec does not like tabs…


Tuning the beamline (USAXS)

There are two items which can be routinely tuned by general user. Ideally these should be done in this order.


Steering the beam. Get control screen (see later in this document how) for steering and then using the M2Y2 (moves beam up and down) and Chi2 (moves beam sideways) try to maximize intensity on I0. You may have to open the Mono Beam Shutter (either manually or through computer control, see later in this document) or remove filters from the beam (see later in this document how to do it). Limit movement to one axis at a time and to only about +/- 5 clicks with the steps preset for you… Note, that these motors do not have backlash correction, so step through the range noting maximum value on I0 and then step into this number and stay there. Use following motor control screen: . Steps in this window are good values unless instructed else.

Monochromator energy. With hutch properly buttoned up type in the command line window “tune_dcmth”. Wait for this macro to finish. The graph on the screen should show nice “Gaussien” peak.

Tune AR/A2rp as necessary (even multiple times).

Tuning the beamline (SBUSAXS)

This procedure is much more involved and if necessary will be done by instrument responsible person. This is list of steps in appropriate order which lead to the best alignment of the instrument.

1. Leave mono beam on (with Ti filter in) and let feedback (using graphite foil) to optimize the beam position

2. Insert Tishler cam and steer beam into the slits

3. Switch off both feedbacks

4. Tune dcm energy

5. Switch on Omega 2 feedback

6. Tune msrp

7. Switch on Chi 2 feedback

8. Tune asrp

9. Tune AR/A2rp as necessary (even multiple times)

Running USAXS

If you were doing radiography before this step and did not do it yet, type in the command line: “useModeUSAXS” and type enter. Check that the hutch is properly buttoned up.


Check the command file (sbusaxs.mac for SBUSAXS) if it is correct.


Comment: about once a day you should change spec file, in which the data are written. This file can become very large if not changed from time to time. This is the procedure:

type in the command line: newsample (enter)

type in generic sample name. Use Your name samples (e.g., Ilavsky samples), this is used for all the tuning macro names…

type new file name. Use: “Month_Day.dat” in number format (e.g. 05_02.dat). Do not forget extension.

accept that the first scan number will be 1 (default).


Do NOT reuse the same spec file name! If you need more, than one spec file in a day, add _1 etc behind the above described name (e.g., 05_02_01.dat 05_02_02.dat etc.).


Type in the command line: “qdo usaxs.mac”.

Check, that everything is running fine (see below).


Checking, that everything is running OK

Following steps tell you, if your USAXS is running fine or if you need to get help.


1. Check intensity in the ion chamber I0. It should be on level which is indicated to you when instructed first. It may vary significantly depending on operating mode of synchrotron. I0 can be 0 at some points of USAXS scan, when instrument is measuring dark currents or changing samples. If the USAXS is running, wait for few minutes. The I0 can jump momentarily to low numbers, when motors on the table are moving. That is normal.

2. Check if the USAXS data look reasonably. Use USAXS plot for this.


If the above items do not look right, check following:

1. Check status of APS synchrotron ring. Was there beam dump?

2. Check if the monochromator feedback is running. This is indicated by presence of dashed green line with text “omega 2 feedback in on” in the UNICAT 33ID Beamline Components control window:


Recovery from various problems

MEDM bug can cause various windows to disappear and user needs to be able to regenerate them. This procedure describes, how to get these windows back from scratch. Please check, which windows still exist and start at step needed. Do not generate multiple copies of windows unnecessarily, since this loads computers and clutters the screens…


Important note: The current version of MEDM allows only ONE copy of each window to exist. If you already have window you want to create on your screen (buried somewhere), nothing happens when you try to recreate it. Look for open windows and find the window you are looking for…

Command window

This is SSH telnet window in which is run program “fourc”, which is used to collect the USAXS data. This window SHOULD NOT be closed by user, as this causes major troubles. It looks like this:


Sometimes, this window is minimized only. Try to locate this window at the bottom of the screen. It should look like this: . There may be multiple copies of this SSH windows at the bottom of the screen and only one of them is the fourc window. Check all of them.

If this window is REALLY missing, major trouble – start calling for help!!!!


Other motor control windows


The MEDM control windows sometimes disappear. They all are served from following window:


If this window is missing get it this way:

Pull up SSH window connected to TEX, found at the bottom of your screen : . In this window type unimenu and push enter:


This will recreate the unimenu window. It may take few seconds – up to minute or so…

If it does not, call for help…


UNICAT 33ID beamline components

This menu serves user feedback controls, steering controls as well as indicates the functionality of omega 2 feedback. This window can be obtained from unimenu , by selecting 33ID… button (2nd from left) and first item in the list (beamline components):


The following window appears:



USAXS plan view

This control screen gives user access to all motors and controls of the USAXS instrument. This can be obtained from unimenu , from the button 33ID… (second from left) by selecting 3rd item (33ID-D General purpose Station) and selecting the item 33ID-D USAXS (MEDM). This generates following window:



Useful tools for USAXS

This floating menu: serves various useful tools for USAXS. User needs this to generate USAXS plot, which provides very good feedback on measured data. This menu can be obtained from the unimenu , from the button 33ID… (second from left) by selecting 4th item (Useful tools for USAXS) and selecting the item 33ID-D USAXS.


Steering controls

If the user needs to steer the beam, steering controls can be found in the UNICAT 33ID Beamline Components control screen:

, under the monochromator are two buttons, in the left button “adjust” the first item is steering: . This serves the following control screen:


USAXS scan parameters screen

This display shows summary of the running USAXS scan. It is very informative. It can be obtained from by selecting button “display USAXS scan term” at the top left corner of this window. The following window is served:



Sample position control (SX + SY)

These controls are necessary for radiography. These motor control screens allow user to move sample paddle to locate samples in the beam. These are served from USAXS Plan View, by pushing button with S (= sample stage) in it (middle above the USAXS instrument), and selecting first item in the pull down menu: , following control screen is served:


The buttons in the left column (with text like “lax:m58:c2:m1 etc) serve control screens for the separate motors:




USAXS plot

This plot window displays live USAXS data as log-log plot, which we are used to. This plot is served from Useful plots for USAXS . There are many options in this menu, most of them are for tunning the USAXS during setup. Select USAXS plot (4th from bottom) to get following plot:

. Since this is not MEDM window, you can have multiple copies of this graph… Not very good idea…

With enough data of course plot looks like standard USAXS log-log plot: .


Editing usaxs.mac file

To edit this file locate running Notetab light program. It should be running and can be found on the bottom of the screen, this is it’s icon: . If it is not runninng, start program by selecting it’s icon from quick start bar at the bottom of the screen: (5th from left, top row)


This program should reopen the latest version of usaxs.mac on its own. Do not modify other files, which may have reopened at the same time!!!! Really bad idea. If you need, you can create your own files in this program and modify those as needed.



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This page last modified: 2006-09-28 10:54 AM