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Subsections


Frequently Answered Questions

If you have questions that are not covered below, please consult the on-line documentation or use our local Google search.

Contact support staff for additional questions.

Data collection

When do I use dose mode?

Dose mode is used to equalize the exposure for images in long experiments by multiplying the exposure time by a dose factor based on the readings from the I2 ion chamber. The dose factor is recalculated before collecting each image.

As a rule of thumb, collecting data in dose mode is advisable when the exposure time per frame exceeds 20 seconds or the total data collection time exceeds 1-2 hours.

It is important to determine the exposure time at the correct beam size and, before initiating data collection in dose mode. Changing the beam size after enabling dose mode will affect the dose for subsequent images (e.g., changing the beam size from 0.2x0.2 to 0.1x0.1 mm$^2$ changes the dose approximately by a factor of 4), and might have undesirable consequences. Adjust the exposure time if necessary after such a change.

Changing the energy also changes the dose, but in a way that partly compensates for the different diffracted intensities at different energies; therefore, dose mode can also be used for MAD experiments to achieve a similar level of exposure at all wavelengths.

Dose mode should not be used when beam attenuation is required, as the ion chamber readings may be too low to calculate a consistent dose factor (in this case, a No beam error will be given by the software).

For more information about dose mode, consult the Blu-Ice documentation.

When should I normalize the dose

The dose should be normalized every time a data collection from a new sample is started. This sets the dose factor to 1. The dose factor may change significantly after a table optimization or change of energy following normalization; the dose factor should not be renormalized in this case unless you really intend for subsequent images to receive a different dose.

How can I convert from wavelength to energy?

In Blu-Ice, click on the units next to the energy input box to toggle between wavelength (Å) or energy (eV or keV).

The program xtalcalc can also be used to convert between wavelength and energy:

  1. Type xtalcalc in a Unix window

  2. Type a value in eV in the Energy box (or click on Defaults) and press Return or click on the Calculate crystal parameters button.

  3. Type in the wavelength and Return or click on Calculate Blu-Ice parameters to calculate the energy.

What is the optimal beamstop to sample distance?

The backstop should be placed at a position where it allows collection of reflections in the 30-40 Å resolution range. At most wavelengths, it will be possible to collect even lower resolution, however, this will be at the expense of additional background scatter that may obscure weak reflections.

Using Web-Ice to calculate the data collection strategy will automatically calculate a reasonable beamstop to sample distance. In addition, the Blu-Ice resolution predictor shows the low resolution limit at the given beamstop and energy values.

You can also use the program xtalcalc to calculate the optimal beamstop distance for the desired low resolution cutoff:

  1. Type xtalcalc in a Unix window.

  2. Type the data collection energy in eV in the Energy box and click Return.

  3. Enter the minimum resolution and click Return. The program will calculate the beamstop to sample distance.

Sample mounting

What is the size of the white box on the beamline monitor?

At maximum zoom, the box is 0.1 mm x 0.1 mm. At medium zoom, 0.25 mm x 0.25 mm and at low zoom it is 1 mm x 1 mm.

Note: The white box in the sample camera video displayed on Blu-Ice represents the beam size as defined by the collimator slits and is therefore more reliable to determine if the crystal is in the beam than the monitor box. Additionally, the size of the Blu-Ice box also changes to reflect the scale at different camera zoom levels.

The automated loop centering leaves the camera near the medium zoom level. Is there anything wrong?

No, this is normal operation. The system uses the medium zoom level to do the alignment, in case large loops are used.

Also, during the crystal screening mode, maximum zoom is used for recording JPEG images of the crystal.

Detectors

What are the slow/fast, binning and dezingering options?

  • For data collection with the Quantum-4 detector, the slow readout mode is more accurate. The fast readout mode should only be used for test images.

  • For data collection using the Quantum-4 detector, binning combines the readout of 4 pixels into one pixel, resulting in a larger dynamic range and better signal-to-noise characteristics at the expense of spatial resolution (but note that on the current SSRL PX beamlines the source is more likely to limit spot resolution than the pixel size). Because non-binning produces large files ( 70 MB), only binning mode is so far allowed for the Quantum-315 detector. There is no binning/unbinning option for the MAR CCD detector.

  • Dezingering should be used for exposure times that are longer than 20 seconds.

Can I display the image header?

You can look at the image header with the Web-Ice Image Viewer .

How do I determine the direct beam position?

The default beam position, should be at the nominal centers of the detectors (within 1 pixel) listed below (in mm):

  • MAR325 CCD: 162.5, 162.5
  • Q315 CCD: 157.5, 157.5
  • Q4 CCD: 94, 94

If the detector is offset, the data collection software writes the true beam center coordinates Cx,Cy to the image header (except for the MAR Image Plate).

Determining data collection strategy

What is a reasonable exposure time for beamline X?

If in doubt, use the default values: in the Blu-Ice Collect tab, click the Default button; in the Screening Tab, click Reset defaults. If your crystals diffract very poorly or you are collecting the images at extra long or short wavelengths you may have to increase the time.

It is recommended to use Web-Ice to determine the optimal exposure time from the initial test shots of the crystal. The time given by Web-Ice is calculated to give a $I/\sigma(I)$ of roughly 3 at the detector edge. As a rough rule of thumb, change the exposure by a factor of 4 to change $I/\sigma(I)$ by a factor of 2.

How long do I need to expose a crystal at SSRL for RIP phasing?

For radiation damage sensitive samples, the best strategy is to do a two-wavelength MAD or SAD experiment without exceeding the maximum recommended dose (use Web-Ice to obtain an estimate of the absorbed dose). Overdosing the crystal results in a unit cell expansion which most often prevents accurate measurement of any kind of phasing signal in the data. Radiation induced intensity difference are no easier to measure than anomalous or dispersive differences in this case.

For some derivatives (e.g., brominated DNA), the heavy atom may become cleaved at very low doses. The program SHARP has been reported to deal well with this particular case, using the loss of occupancy of the anomalous scatterer to enhance MAD or SAD phases, as long as the total dose is kept to a reasonable value.


Problems during data collection

How can I monitor the SPEAR beam?

The beamline status and current are displayed in the Blu-Ice status barhttp://smb.slac.stanford.edu/facilities/software/blu-ice/getting_started.html#Status_Bar.

Additional information about SPEAR (including status of all beamlines and the 24-hour fill history) is displayed on a monitor at the beamline (top left corner of the console) and on the SSRL SPEAR Web page. See also ''Monitoring the SPEAR status remotely''

How often is the beam refilled?

Currently SPEAR is topped up every 8 hours, at 6:00, 14:00 and 22:00. The top up lasts only a few minutes. Occasionally the stored beam is lost during injection and a longer refill is required.

After the refill it takes a couple of additional minutes for the temperature of the beamline optics to stabilize.

Will data collection pause during beam refills?

During data collection, the beam status is monitored by the beamline control software. Data collection will stop when SPEAR is down and restart when the temperature of the beamline optics has stabilized after the beamline is reopened.

A message is displayed in the Blu-Ice status box while the beam is stabilizing following an injection.

Additionally, the beam in the hutch is monitored before each image is collected for both time and dose modes.

How does the search and reset procedure work?

Completely search the hutch for persons before activating the search reset. The hutch door must be closed and locked before the search alarm stops ringing, otherwise the procedure must be repeated.

Is there beam in the hutch?

Check that the shutter switch is open on the key panel in the control rack (all green LEDs should be lit). Look at the ion chamber readings to determine if there is beam in the hutch. If you are not sure what the ion chambers readings are supposed to be, open and close the main beamline stoppers. When the stoppers are open the readings should be several times higher.

If the reading on I0 looks normal but the ion chamber I1 and I2 readings are low or negative and do not change significantly when opening and closing the stoppers check if the beam is attenuated or a small beam size on the Blu-Ice hutch tab. If the beam is not attenuated and the beam size has not changed, click on Optimize Beam to realign the table. If the beam optimization does not solve the problem, call support staff.

Figure 42: Ion chamber readings
\includegraphics[width=0.6\textwidth]{images/ionchambers.ps}

Why do I get blank diffraction images?

To determine the cause of blank diffraction images, follow these steps:

  1. Verify that there is beam in your sample (see the previous question).

  2. If there is no image displayed, try opening the image with a different program (e.g, ADXV, Mosflm) If the image looks only blank on Blu-Ice or Web-Ice, the image server may have crashed. Contact support staff (please, send an e-mail during non-working hours, as this problem does not affect data collection).

  3. Check the contrast in the image display: Images with no diffraction spots displayed at a high contrast level can hide diffraction features.

  4. If you see very weak scatter on the image, verify that the exposure time is not too short - this can happen if dose mode is on, and the dose factor is very small.

  5. If the image is truly ''flat'' (no beamstop shadow nor variation in the background level of the image at any contrast level), verify that there is not a cover on the detector.

  6. If nothing is blocking the detector look at the shutter controller to determine if the shutter is opening. The switch on the controller should be on "auto" and a red LED light should light up when the shutter is open, as shown in fig.. Remote users can use the ''panel'' camera to view the shutter controller. In addition, when the shutter opens you should be able to see an increased reading for the I_beamstop beam monitor. The I_beamstop reading will be low at long wavelengths (low energies). Verify that there is beam on the beamstop by going to a shorter wavelength (higher energy).

    Figure 43: Shutter controller showing open shutter status
    \includegraphics[width=0.5\textwidth]{images/shuttercontrol.ps}

  7. If there is diffuse diffraction but no spots, check the centering of the crystal. Open up the slits to increase the beam size and collect images at different crystal orientations. If you get diffraction with a large beam size or at some phi positions but not others, the phi axis may be misaligned. Contact support staff.

  8. If there is no difference with large slits or at different phi positions, the crystal may not diffract (even if it was diffracting previously). Save the crystal and take a shot of a diffracting sample (for example, the Si powder sample in the toolboard). If you do not observe any diffraction from any sample, contact support staff.

Why can't I open Blu-Ice?

The first time you log in to Blu-Ice it will request your password. Make sure that it is typed correctly. If you cannot log in, contact the user support staff and let them know what Unix account you are using.

If you cannot start Blu-Ice from the icon in the XFCE menu:

  1. Open a terminal on the local workstation or NX client.

  2. Log in to a different beamline workstation. For example, if you are trying to open Blu-Ice from bl92a, log in to bl92b or bl92c. Use the command:

    >ssh bl92a

    The NX client opens Blu-Ice on the ''c'' workstation, so in that case use the ''a'' or ''b'' computer.

Why is Blu-Ice not responding?

  • Verify that the Blu-Ice window is active.

  • If some buttons are inactive (grayed out) move the mouse over the button. Blu-Ice will display a message explaining why the button is inactive. If the message tells that the control software for a hardware component is off-line (''DHS off-line'') contact support staff.

  • An emergency stop button (yellow) may have been depressed accidentally. To reset the motors, press the green motor reset button.

  • Verify that the beamline stopper is open.

  • If the entire Blu-Ice interface fails to respond, make a note of what the program was doing when the fault happened and check for error or warning messages in the Unix shell. Exit the Blu-Ice client and start a new one. If the fault persists, call support staff.

  • Sometimes, a computer crash or a network problem can hang the system. In this case, other programs and processes will also be affected. If the window manager program is hanging, log on to the host computer from another terminal and kill the processes. To list processes:

    >ps -u "your_id"

    and kill them with

    >kill -9 "process_id"

  • If all the computers at the beamline are hanging or data collection will not proceed, the file system may have crashed. Contact support staff.

What does the message ''Detector error'' mean?

A detector error message in Blu-Ice can have many different causes; although often staff intervention is required in order to continue data collection, it is a good idea to retry the image collection before calling staff, as some errors (e.g., a transient network glitch) do not disable the detector permanently.

Important: Note that the ''Detector Error'' message will still be displayed after a problem with the detector has been fixed; the message will only disappear once an image has been collected without errors.

When should I optimize the beam?

It is advised to optimize:

  • After changing the wavelength from the Hutch tab. Automatic optimization is performed after wavelength changes during MAD data collection.

  • After changing the beam size.

Automatic optimization is also performed at regular intervals during data collection and therefore, manual optimization should not be necessary.

Important: Optimization immediately after a refill is not advised: always wait for 3 minutes before attempting manual optimization (this allows the beam position to stabilize while the optics are warming up).

Data processing and graphics software

Why can't I run graphics software?

Graphics programs must be run directly on the local beamline Linux machines (eg. bl15a, bl15b and bl15c on BL1-5). They will not run on the blcpu computers. Check that the Unix shell is opened directly on the local machine, rather than using ssh or rlogin to connect remotely.

I get an HTTP error when trying to display or refresh a page in Web-Ice

Often this will be a transient server glitch. Try refreshing the page again. If the problem persists, contact Ana Gonzalez (use e-mail outside working hours)

Why doesn't program X run?

Most crystallographic software packages are only installed on the compute servers blcpu1, blcpu2, blcpu3, etc, and not on the local beamline computers. Most graphics programs are installed only on the local beamline workstations.

Why is Mosflm/HKL2000/other running slow?

Make sure that you are using a fast data processing computer. Blcpu1l is the fastest, followed by blcpu5 and blcpu4. Users currently collecting data at the beamline have priority on these machines.

Check the relative load of the data processing server as described in ''data processing environment''.

Why can't I autoindex my images?

The detector may have been offset from Blu-Ice: Check the detector positioner vertical and horizontal values in the Blu-Ice hutch tab. If they are not 0, look at the center coordinates in the image header (the Web based software Web-Ice can be used to display the image header).

  • Web-Ice knows about the detector coordinate system and can use the image header coordinates directly for auto-indexing.

  • The Mosflm and HKL2000 coordinate systems are related to the beam center coordinates (Cx,Cy) by the following equations:

    x = detector-width - Cy

    y = Cx

    The mosflm script used at the SSRL automatically transforms the beam coordinates. For HKL2000 and XDS you must provide the offset center as explained in the documentation.

Indexing may also fail if the diffraction is weak, if there are many ice rings or if there is a double lattice. Editing the spots manually in Mosflm or HKL2000 often circumvents these problems. Web-Ice uses a different spot-finding algorithm and it is worth trying if other software fails.

If the diffraction pattern is misindexed (this should be very rare, but is a possibility if the spots are very close and the r-merges after scaling are above 20 or 30%) try using Web-Ice (Web-Ice does not assume that the input center is correct, but searches for the optimal coordinates over a small area).

You may also determine the accurate center position by following these steps:

  1. Move the detector to the distance used for data collection.

  2. If the resolution at the edge of the detector is 3Å or higher, use the Si sample, otherwise use the polyethylene sample. Both samples are located in the same compartment on the beamline tool board.

  3. Collect a diffraction image. For the Si sample, use a delta phi of 15 degrees and 5 s exposure time. For the polyethylene sample, use a delta phi of 0.02 degrees and a 1 s exposure time. If the detector saturates, attenuate the beam.

  4. Run the program center on one of the blcpu servers to calculate the direct beam position from the image.

Important: The beam center position in the image header should be accurate to within 0.1mm. In the extremely rare event that it is off my a larger amount, make sure to tell user support staff.

How do I display the JPEG snapshots of the crystal?

You can use the screening tab or the image tab in Web-Ice to display the crystal snapshots.

You may also use the program display (from a Linux or Unix shell).

Are the International Tables for Crystallography available?

On-line Space Group diagrams are available at
http://smb.slac.stanford.edu/facilities/software/spacegroups/. This site is for local access only; the NX Client can be used to view the tables remotely.

The full International Tables are available at
http://it.iucr.org/. The IUCr site is fully accessible from SSRL or the NX client (or off-site if your local institution has a license).

Is it OK to leave files on the /data disk?

Users are responsible for backing up by their data by the end of their beam time. Images stored on the /data disk can be deleted at any time. Special requests to keep files on /data should be made to support staff. The /home area can be used to store small files indefinitely.


Remote access


How can I monitor the SPEAR beam remotely?

The beamline status and current SPEAR intensity are displayed in Blu-Ice. The video tools in Blu-Ice and Web-Ice can also be used to look at the beamline SPEAR monitor; in addition, the SPEAR status and fill history can also be accessed via the web.

For updates or inquiries about SPEAR you can call the duty operator 24/7 at 650 926-4040, or the beam information line at 650 926-BEAM (2326).

Can others view me using the beamline video cameras?

Yes, in general, staff can view all beam line video feeds at any time. Anyone with access to your account and password can also view the beamline video feeds. However, the cameras can be turned off at the beamline (see the Blu-Ice video documentation.)


HKL2000 displays a screen size error

In order to run HKL2000, the NX client window must be at least 1100 x 900 pixels. If HKL2000 gives the error ''HKL2000 requires screen width larger then 1100 and screen height larger then 900 (sic)'', stretch the NX client window by left-clicking on a corner and moving out the mouse. Old versions of the NX client do not support dynamic resizing of the window. In this case, it is possible to reconfigure the window size (but updating to the latest version of the client is strongly recommended instead):

  1. Exit your current NX session.

  2. Open the NX Client as described in the installation instructions and Click on the Configure button.

  3. Find the Display options under the General menu and select ''Available Area''. If you are already using this option, select ''Custom'' instead and use the W and H input boxes to select the appropriate size.

  4. Save the configuration and restart a NX session.

The Mosflm GUI does not fit in the NX client window

Make sure that the NX client display is set to ''Available area'' (see above), and use the command mosflm_SD to run Mosflm (SD stands for ''small display'').

I cannot open an ADXV window from Blu-Ice

There is a limit on the number of ADXV processes allowed to run on the NX server in order to stop it from running out of memory (currently the limit is 5). To inspect new image, close some old ADXV windows. You can also use Web-Ice to inspect the images.

Why can't I connect to the NX server?

  • Check for typos in the server name: smbnxs1.slac.stanford.edu or smbnxs2.slac.stanford.edu.

  • Someone else in your group may be accessing the server using the same session name. Try reconfiguring your NX client and provide a different session name (e.g., if you named your session SMB, as in the example in the configuration instructions, try using SMB1 instead).

  • If you see a dialog box with the message ''Resuming suspended session'', which then disappears, the cause of the problem is trying to connect to a hung session. See below.

  • Occasionally an NX server may be down for maintenance and upgrades. If smbnxs1 does not respond, try reconfiguring your client to connect to smbnxs2 instead, and vice-versa.

    Important: If the NX session crashes frequently, verify that you are running the latest version of the client (3.0.0 or higher). You can find the version number in the ''About'' tab in the client configuration options.

Why can't I see staff phone numbers on the web?

Most staff phone numbers are only visible from on-site only. They can be viewed remotely by opening a browser within the NX Client.


Can I terminate an NX session that is hung?

Although the NX Client software has a feature that allows you to kill a process, sometimes it does not work. In addition, sometimes the software will not allow you to open a ''new'' session and automatically reconnects you (and others using the same account) to the hung session. You can try to connect to the NX server using ssh and search for running sessions:

ssh smbnxs2.slac.stanford.edu

ps -fe | grep $USER | grep nxagent

and then kill the nxagent process:

kill -9 "process_id"

If this does not work, contact support staff.

Computers

Can I change the default settings for my SSRL account?

Click on the Settings icon in the Xfce panel to access the Settings Manager GUI. Exception: Use only the Blank Screen as a screen saver (animated screen savers use a lot of CPU, which can affect remote access through the NX client).

The previous group left the workstations locked. How do I log in?

You can log out the previous user with the keys Ctrl-Alt Backspace. Please do not do this unless you are certain that the previous group or support staff have finished working at the beamline. If in doubt, call support staff.