Quick data processing with iMosflm
This is a brief description of how to use imosflm to quickly
process and scale data to get an idea of the quality of the
data. For a more complete description of the program and its
advanced features, visit
Tutorial site at MRC-LMB Cambridge.
- Start by logging in to one of the data processing servers at SSRL
as described in
Guide. Mosflm and other processing programs can be CPU and memory
hungry and therefore are not installed in the NX servers and beamline
- Create a subdirectory in your /home or /data area where you want
to store the results (you can also use an existing directory) and cd to
that directory, eg:
|Launch the GUI by typing "imosflm" in that directory. When the GUI
appears, start by creating a new session by clicking on the top left
icon (you can hover with the mouse over the icons to find out what
they are). Creating a new session will allow you to see the results
and add more files later on.
|Next, add the images in the data set; click on the 4th icon. You
can use the navigation icon to select the directory in your /data area, type
the directory name in the input window or a mixture of both to
locate your images.
|Then, click on one of the images (usually the first
one) and the "Open button". This will import all the images with the same
root name. The program will also open the selected image in a
|You can use the "masking tool" and "circle fitting"
in the image display window to mask out the beamstop shadow. The
pixels in the detector seams have a special value and the software
ignores them so you do not have to do anything about them.
Go back to the main window and click on the "Autoindex" task
icon. The program will select automatically the optimal images to
autoindex and default parameters. After autoindexing, it will
select a space group (you can override it) and provide an estimate
for the mosaicity.
|Next, refine the unit cell. In principle you can
refine the unit cell during postrefinement, but refinement
will be more stable if you do this step first. Once the
program has selected the defaults, click on the "Process"
button. The program will display the refined parameters for
all the images. They are usually in two different wedges, so
some discontinuity in the parameters is expected. Inspect the
image display to make sure that the predictions match the
position of observed spots.
|Select the integration task to integrate and
postrefine the images. Note that the program will fix the unit
cell parameters by default. The program will display the
results as integration and refinement progresses.
|Inspect the results. If your data are reasonable,
you may still see some warning messages about the processing,
which you may want to inspect eventually. Poor refinement
parameter and integration statistics and critical error
messages suggest that there is a problem with the data or the
processing itself. If this is not the case, press the "QuickScale" button to run symmetry analysis, scaling, merging and
data truncating. This may take some time depending on how
many images and reflections you have. After a while, the
results will be displayed in a separate window and you will
be able to make an assessment about the quality of your data set.
The log and output files from all the steps of the processing will be stored in
the directory you are running the program from. All the output files
are written in mtz format. Files generated by the program are given
an unique name based on the time and date or in the root name of the
input images. Here is a list of the files:
- mosflm .lp, .mat and .sum files: contain a detailed processing
log, orientation matrix and processing summary.
- ANOMPLOT, ROGUEPLOT, ROGUES, NORMPLOT, CORRELPLOT and SCALES are
auxiliary and plot files generated by Aimless.
- The pointandscale log contains the Pointless, Aimless and
- The mtz file of the form "image name".mtz is the integrated
intensities from mosflm. The pointless_"image name".mtz file has
unmerged sorted reflections in the correct space
group. aimless_"imagename".mtz has scaled and merged intensities and
ctruncate_"image name".mtz contains the intensities and calculated
amplitudes (a "unique" version of this file, with a free set
selected, is also written out.
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