New versions of iMosflm (1.0.5) and Mosflm (7.0.7) are now available from the MRC LMB web site (32nd December 2010). ---------------------------------------------------------------------- Changes since 1.0.4 / 7.0.6 We have concentrated on making iMosflm and Mosflm more robust and easier to use; they should fail less frequently than before, especially when working with datasets of marginal quality. We have implemented one or two major enhancements in iMosflm to help make processing an even smoother experience. There are some new features in Mosflm that are not yet available in iMosflm; they are available for testing purposes but need to be optimised further before being included in iMosflm. Pilatus images: Note that Pilatus detector images collected at beamline ID29 at ESRF can now be processed. Also, the default rejection criterion "too steep background gradient" has been changed, the previous default led to many reflections being flagged as badspots on very weak Pilatus images. In addition, the "Null pixel threshold" value is now correctly set in iMosflm to -1 (ipmosflm run standalone set the correct value) which will also improve processing of very weak images. There is an important change to the mosaic spread refinement. Previously the mosaic spread was often underestimated for very fine sliced images (oscillation angle < 0.2 degrees) typically collected with Pilatus detectors, leading to a negative partial bias in SCALA. The new algorithm gives significantly better results, but can in some special cases (typically very split spots, arising from two or more lattices in a very similar orientation) result in a steadily increasing mosaic spread as more images are integrated, eg starting at 0.8 and going up to over 1.5 degrees. This behaviour can often be avoided by using the new parameter 'Size of smaller fraction of summed partials' in the Processing Options ~ Advanced refinement tab. This now defaults to 0.25, but setting it to 0.5 (the default in previous versions of mosflm) will often produce a stable mosaic spread refinement in such circumstances. The appropriate keywords for Mosflm are: POSTREFINE PARTITION Where is in the range 0.2 to 0.5. Enhancements to the iMosflm GUI (Version 1.0.5) =============================================== New features and improvements: * Open several or a range of images with CTRL-click or SHIFT-click, respectively. * Display of the active mask for images from Rigaku detectors can now be toggled. * Plots of the number of overloads, spatial overlaps and 'bad spots' for each image can now be displayed . * Warning messages have been enhanced with feedback from Mosflm * Automatic spot finding can be disabled when entering Autoindexing. * QuickScale can now be run either treating data as anomalous or ignoring anomalous data in Scala. Symmetry known to iMosflm can now be passed to Pointless when running QuickScale. * The program Ctruncate is now run automatically following Scala when using the QuickScale button. * Site specific parameters can be read from a saved Mosflm file (.mos) on startup using the ~init command line argument. * The 'View' menu has been renamed 'Settings' in the main iMosflm interface window. The small cross in the Warnings pop-up box has been replaced by a green, tick icon. * A new entry field, 'Size of smaller fraction of summed partials', has been added to Processing options ~ Advanced refinement. With its default, initial value of 0.25 this will set the proportions that partials are divided into for post-refinement so that 0.25 of the intensity is in part one and 0.75 in part two. Values from 0.2 to 0.5 are permitted. Previous default value was 0.5. Further details =============== * To open selected images, check the 'Selected images only' box in the Add images window and use Control-Click to (de)select one image and Shift-Click to (de)select a range of images from the one currently selected. Additionally, Control-a now selects all images displayed (double-clicking on an image selects all images matching the filename template). * To toggle the Rigaku active mask use the button in the toolbar of the Image display window. * Plots of the number of overloads, spatial overlaps and 'bad spots' for each image are displayed in the usual way by clicking on the additional three items in the bottom left-hand corner of the Integration pane. * Warning messages displayed in the pop-up summary box can now be double-clicked to reveal more information returned by Mosflm (if available). The 'detail' box is closed by clicking outside of it. The warning summary pop-up must be closed by clicking again on the Warning alert area in the bottom right-hand corner of the iMosflm main window. * A checkbutton has been added to Settings ~ Processing options ~ Spot finding to select automatic spot finding when entering the Autoindexing pane. The state of this checkbutton (and that for 'Automatically index after spot finding') are saved to the user's profile between runs. The Index button is inactive unless images have been chosen for spotfinding and entered. * QuickScale was previously always run in a way that separated Friedel pairs when calculating merging statistics (equivalent to ANOMALOUS ON in SCALA). However, when scaling a relatively small phi range (e.g. 25 degrees) from a low symmetry (e.g. monoclinic) spacegroup, this can result in the table that reports Rmerge etc. as a function of resolution being empty (as only anomalous pairs have been measured). One then has little idea of the data quality. This is important when dealing with data from microcrystals where only a small phi range can be collected from each position (or crystal) because of radiation damage or when trying to assess data quality when only part of the data have been collected/integrated. * Symmetry chosen within iMosflm can now be passed to Pointless when running Pointless+Scala from the QuickScale button to obtain statistics for the selected symmetry. Checkboxes for both options have been added to the Advanced integration tab in Processing options. This feature requires you have a reasonably up-to-date Pointless version. * The program Ctruncate calculates a number of statistics from the intensity data, such as moments, cumulative intensity distributions and the Wilson plot. The output produced in a web browser by Baubles has graphs which can be used to assess data quality and to check for possible twinning. The Javascript options in your browser may need adjustment to see these plots. * Various site-specific parameters can be set in the Settings sub-menu tabs then saved as a .mos file in the usual way. This file can be read at start-up with the ~init command line argument. Bug fixes ========= * All images are now loaded when '+' occurs in filename template. Improved pattern matching of the template prevents non-image files being included. * RMS residual (Distance or Y scale) are now plotted for the final image in the Cell refinement summary plots in the bottom right-hand corner of the pane. * A Tcl error has been trapped when attempting to index an image with no spots. A trap has also been added for Tcl/Tk 8.4.13 wherein the display of images is broken. * Phi missetting angles for the first image of a new sector are now correctly plotted in the Cell refinement pane during refinement and correctly displayed in the Images browser following refinement. Previously, they were assigned from the last image of the previous sector. Additionally, the negative sign is no longer lost when editing a negative missetting angle value by clicking a highlighted line in the Images browser. * A warning has been added if the detector distance read from the image header is zero. The user is invited to enter the correct value. * Wherever possible, the iMosflm interface has been re-enabled following a Mosflm error/restart situation. * Errors in plots caused when choosing fewer than eight images for Cell refinement have been addressed. * If Mosflm returns any value which has overflowed its formatted field as '****' in the XML, iMosflm will attempt to locate the XML tag name and pop-up a warning message. * The correct value for the null pixel threshold is now sent from Mosflm for all detectors (including Pilatus, where it is -1). Spots containing a pixel value lower than this are ignored. The maximum background gradient is now also read from the image header and set correctly for Pilatus detectors (0.06) and other detectors (0.03). These values are shown in the Advanced integration tab in Processing options. * If the checkbox Multiple MTZ files (1 per block) was checked in the Processing tab of Processing options this option is now correctly turned off when un-checking the box. * File names for the saved Mosflm summary and print files have been renamed on Windows to have more sensible file types (viz. mosflm__