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Subsections
Troubleshooting
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.
HTTP errors may be caused by transient glitches communicating
with the server. Try again. If the problem persists, tell the user
support staff.
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.
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).
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.
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.
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:
- Collect 1 degree oscillation images at 0, 1, 2, 3 degrees, and
90 degrees.
- 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.
- 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.
- 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?
- Inspect the results saved to your disk area using the
[ Details ] link.
- 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...
See the RADDOSE documentation
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.
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