iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM

iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM

2011 | T. Geoff G. Battye, Luke Kontogiannis, Owen Johnson, Harold R. Powell and Andrew G. W. Leslie*
The paper introduces iMOSFLM, a new graphical user interface (GUI) for diffraction-image processing with MOSFLM. iMOSFLM simplifies data processing by dividing it into sequential steps, each with its own display pane for parameter control and feedback. It automatically sets integration parameters but allows detailed control for experienced users. The interface includes tasks for image display, indexing, strategy calculation, cell refinement, integration, and history. Key parameters and success assessment methods are discussed. MOSFLM is a program for processing diffraction data collected using the oscillation method. A previous GUI based on X11 routines had limited functionality and graphical quality. iMOSFLM, a Tcl/Tk-based GUI, addresses these issues by providing an intuitive route to data processing, guiding inexperienced users and offering full functionality for experienced users. The iMOSFLM GUI has an overall structure where tasks are managed through panes. Each task has its own pane for parameter setting and result display. The Image Display window allows inspection of diffraction images, including predicted reflections and masked areas. Drop-down menus provide access to session and view settings, including experimental and detector parameters. The Indexing pane allows spot-finding and indexing. Parameters for spot-finding include search area, threshold, and rejection criteria. Auto-indexing uses an FFT-based algorithm to determine the crystal lattice. The success of indexing is assessed by inspecting predicted reflections and checking the positional residual. Common causes of indexing failure include errors in direct-beam coordinates, multiple lattices, radiation damage, and incorrect spindle rotation direction. The paper discusses how to address these issues, including manual adjustment of the direct-beam position and using a two-dimensional grid search. The Strategy pane calculates an optimal data-collection strategy based on the Laue group and crystal orientation. It provides statistics on data completeness and multiplicity, and allows adjustment of the rotation range to avoid spatial overlaps. The Cell Refinement pane refines cell parameters, crystal orientation, and mosaicity based on post-refinement procedures. It uses a post-refinement procedure to provide more accurate values, especially for data with resolution better than ~3.5 Å. The Integration pane allows control of data integration, symmetry detection (POINTLESS), and preliminary scaling (SCALA). It writes results to a CCP4 MTZ file and provides statistics on intensity and other data quality indicators. The History pane displays a tree structure of all operations in the current session and provides access to the MOSFLM logfile. The paper concludes that iMOSFLM provides an intuitive approach to processing diffraction data, with ongoing development to improve performance and add new features. The software is distributed with the CCP4 package and is available for Windows, Mac OSX, and Linux platforms. The work is supported by CCP4 and BBSRC.The paper introduces iMOSFLM, a new graphical user interface (GUI) for diffraction-image processing with MOSFLM. iMOSFLM simplifies data processing by dividing it into sequential steps, each with its own display pane for parameter control and feedback. It automatically sets integration parameters but allows detailed control for experienced users. The interface includes tasks for image display, indexing, strategy calculation, cell refinement, integration, and history. Key parameters and success assessment methods are discussed. MOSFLM is a program for processing diffraction data collected using the oscillation method. A previous GUI based on X11 routines had limited functionality and graphical quality. iMOSFLM, a Tcl/Tk-based GUI, addresses these issues by providing an intuitive route to data processing, guiding inexperienced users and offering full functionality for experienced users. The iMOSFLM GUI has an overall structure where tasks are managed through panes. Each task has its own pane for parameter setting and result display. The Image Display window allows inspection of diffraction images, including predicted reflections and masked areas. Drop-down menus provide access to session and view settings, including experimental and detector parameters. The Indexing pane allows spot-finding and indexing. Parameters for spot-finding include search area, threshold, and rejection criteria. Auto-indexing uses an FFT-based algorithm to determine the crystal lattice. The success of indexing is assessed by inspecting predicted reflections and checking the positional residual. Common causes of indexing failure include errors in direct-beam coordinates, multiple lattices, radiation damage, and incorrect spindle rotation direction. The paper discusses how to address these issues, including manual adjustment of the direct-beam position and using a two-dimensional grid search. The Strategy pane calculates an optimal data-collection strategy based on the Laue group and crystal orientation. It provides statistics on data completeness and multiplicity, and allows adjustment of the rotation range to avoid spatial overlaps. The Cell Refinement pane refines cell parameters, crystal orientation, and mosaicity based on post-refinement procedures. It uses a post-refinement procedure to provide more accurate values, especially for data with resolution better than ~3.5 Å. The Integration pane allows control of data integration, symmetry detection (POINTLESS), and preliminary scaling (SCALA). It writes results to a CCP4 MTZ file and provides statistics on intensity and other data quality indicators. The History pane displays a tree structure of all operations in the current session and provides access to the MOSFLM logfile. The paper concludes that iMOSFLM provides an intuitive approach to processing diffraction data, with ongoing development to improve performance and add new features. The software is distributed with the CCP4 package and is available for Windows, Mac OSX, and Linux platforms. The work is supported by CCP4 and BBSRC.
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