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 the iMosflm Tutorial site at MRC-LMB Cambridge.

  • Start by logging in to one of the data processing servers at SSRL as described in the User Guide. Mosflm and other processing programs can be CPU and memory hungry and therefore are not installed in the NX servers and beamline control machines.
  • 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:
  •  cd /data/ana
     mkdir MOSFLM-DEMO
     cd MOSFLM-DEMO
    
  • 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 separate window.
  • 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 CTruncate logs.
    • 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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