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Up: Web-Ice
Previous: Preferences
Subsections
  • Q. I have typed the name of the image file in the File input box, but the JPEG file is not displayed and the right frame displays ''Failed to load image header''
  • Q. I get an HTTP error when trying to display or refresh a page
  • Q. In the Autoindex tab, the ''Runs'' table does not get loaded properly (the fields for the runs are empty); when trying to display the run contents, the browser displays an impersonation server error
  • Q. When I try to collect images or export a run to Blu-Ice, I get an error message saying that there are too many runs already. What does this mean?
  • Q. When I change the oscillation angle before Exporting the run to Blu-Ice, the exposure time changes when I recalculate the dose
  • Q. Autoindex/Screening fails with a MOSFLM error. What has happened?
  • Q. What do the System Errors displayed in the Spreadsheet mean?
  • Q. My crystal is pseudo-cubic, with the true symmetry being rhombohedral. I want to use Web-Ice to calculate the phi-rotation strategy, so I tried entering the known Laue group and unit cell in to the Autoindex run setup. This failed. Autoindexing also failed when I gave just the Laue group. How can I get the right strategy?
  • Q. How can I verify that the data collection strategy is calculated correctly?
  • Q. My buffer contains 1M NaCl and I have very small crystals. How do I account for that in the dose calculation?
  • Q. Why is the predicted resolution lower than I expected?


Troubleshooting

Q. I have typed the name of the image file in the File input box, but the JPEG file is not displayed and the right frame displays ''Failed to load image header''

Make sure that the image exists (ie, no typos) and is readable.

You must type the full path to the image input window - alternatively, try using the file browser in the bottom frame.

Q. I get an HTTP error when trying to display or refresh a page

HTTP errors may be caused by transient glitches communicating with the server. Try again. If the problem persists, tell the user support staff.

Q. In the Autoindex tab, the ''Runs'' table does not get loaded properly (the fields for the runs are empty); when trying to display the run contents, the browser displays an impersonation server error

If this problem happens, try reducing the number of runs displayed per page in the autoindex tab options in the Preferences tab. If the problem persists, there may be a large number of users trying to connect to the impersonation server. Let the user support person know about this.

Q. When I try to collect images or export a run to Blu-Ice, I get an error message saying that there are too many runs already. What does this mean?

There is a maximum limit of 16 data collection runs in Blu-Ice. When all the runs have been used up, Web-Ice will give this error message. If this happens, open a Blu-Ice window (via the NX client if you are a remote user) and delete some runs manually (doing this will NOT delete or affect the data collected by these runs).

Q. When I change the oscillation angle before Exporting the run to Blu-Ice, the exposure time changes when I recalculate the dose

The exposure time should be proportional to the oscillation angle; some people forget to adjust the former when modifying the latter, that's why the software will change it. However, if you really do intend to change the exposure per degree, just edit the exposure time. After that, you will be able to change the oscillation angle without automated corrections of the exposure time.

Q. Autoindex/Screening fails with a MOSFLM error. What has happened?

After autoindexing the images, LABELIT runs MOSFLM to integrate the images. This serves to confirm that the lattice chosen by LABELIT is correct and provides additional information about the crystal diffraction properties and qualities. Unfortunately, the integration step sometimes fails, particularly for poor crystals. If this happens, you can see the autoindexing results from LABELIT by following the [Details] link in the Autoindex Tab or in the Cassette Details page in the Screening Tab, and clicking on the labelit.out file.

For experienced MOSFLM users: The Details page also contains the input and output MOSFLM files (called index## and index##.out, with the number corresponding to different LABELIT solutions. Often the error will happen when integrating the triclinic solution, i.e., examine the index01.out file. You might be able to integrate the images by tweaking the input parameters in the input files.


Q. What do the System Errors displayed in the Spreadsheet mean?

In most cases, a system error indicates that a autoindex solution could not be found; a ''No_Indexing_Solution'' error message is given in this case, followed by the specific cause:

  • Too few non-ice spots (x) in image #

  • Too few candidate Bragg spots (x) in image #

  • Too few good Bragg spots (x) in image #

    These three errors simply indicate that there are not enough spots for reliable autoindexing. Inspect the crystal JPEG image in the Screening Cassette Details page to verify that the crystal is hit by the beam (the crystal should be roughly in the middle of the image). Re-mounting the crystal and centering manually (and adjusting the beam size to decrease the background) may help. Weakly diffracting crystals may need longer exposure.

    See the LABELIT manual for a detailed explanation of how spots are chosen for autoindexing.

  • Too few unimodal Bragg spots (x) in image #

  • couldn't find 3 good basis vectors

    There errors usually indicate high mosaicity or low crystal overall quality.

Occasionally Autoindex may fail with a MOSFLM error. See previous Question.

Q. My crystal is pseudo-cubic, with the true symmetry being rhombohedral. I want to use Web-Ice to calculate the phi-rotation strategy, so I tried entering the known Laue group and unit cell in to the Autoindex run setup. This failed. Autoindexing also failed when I gave just the Laue group. How can I get the right strategy?

In many cases entering the known symmetry and cell is a good way to handle pseudo-symmetry. However, this is a very special case. As shown by the LABELIT indexing log file, your crystal can be indexed in four possible rhombohedral settings, depending on which body diagonal of the primitive cell is taken as the threefold. These four cases cannot be distinguished until the data are integrated and symmetry-related intensities are compared. Still, if radiation damage is a problem, there is a way to identify the threefold with minimal initial data. Follow these steps:

  1. Collect 1 degree oscillation images at 0, 1, 2, 3 degrees, and 90 degrees.

  2. Use Web-Ice Autoindex Tab to index on the 0 and 90 degree frames. Now navigate to the Details button to display the name of the Unix directory that contains the processing results.

  3. Open a Unix command shell and change to that directory. Issue the command
    labelit.rsymop 1 4
    this integrates the first 4 degrees of data and helps identify the correct setting.

  4. Again in Web-Ice, return to the Autoindex results, and hit the Setup button. Request the additional integration of the correct solution (verify which solution number corresponds to the correct setting in the Autoindex solution list), and hit ''Submit''. When this is complete, proceed to the Strategy button, select the correct solution number in the solution selection box, and read off the optimal phi-rotation range from there.


Q. How can I verify that the data collection strategy is calculated correctly?

  1. Inspect the results saved to your disk area using the [ Details ] link.

  2. If you do not agree with the input used to calculate the strategy (e.g., mosaicity, resolution limit) or other assumptions made about the sample, you can edit the input command files written out by Web-Ice and re-run the programs from the command line on the pxproc computers:

    • To run BEST: edit the file run_best.csh in the subdirectory solution##/'space-group (if BEST is used as the Strategy Program) or in the BEST subdirectory (if MOSFLM is used as the Strategy Program); then run it as ''source run_best.csh''. Consult the BEST documentation

    • To run the MOSFLM strategy: edit strategy.mfm and/or strategy_anom.mfm (if MOSFLM is used as the Strategy Program) and testgen.mfm in the solution##/'space-group' subdirectory, and run them as ''source strategy.mfm'' (for example).

    • To recalculate the dose: edit the run_raddose1.csh file in the solution##/RADDOSE subdirectory and run RADDOSE by typing

      source run_raddose1.csh

      Note that for MAD experiments you will also have to run run_raddose2.csh and (if using 3 energies) run_raddose3.csh to calculate the correct dose at each of the energies used in the experiment.

      See also next question...

Q. My buffer contains 1M NaCl and I have very small crystals. How do I account for that in the dose calculation?

  • Open the run_raddose1.csh file (see previous question). Add the line

    SATM Na 1000 Cl 1000

    (i.e., the element(s) in your sample heavier than oxygen and its concentration in mM).

  • You can also supply the true size of your crystal (in the CRYSTAL line - the first number should the dimension along the spindle) and the number of heavy atoms per monomer (under PATM) if you have not defined this already using the web interface.

  • Re-run RADDOSE as explained in the previous question.

See the RADDOSE documentation

Q. Why is the predicted resolution lower than I expected?

If the resolution limit is lower than the target resolution, use a longer exposure time for the test images. Recollect the test images (using the Recollect button) and increase the exposure time.


Technical questions: Webmaster    Content questions: Ana Gonzalez

Last modified:Tuesday, 13-Aug-2019 14:45:10 PDT.