[ccp4bb] iMosflm version 1.0.6 Mosflm version 7.0.8
Dear all We are pleased to announce the public release of new versions of iMosflm and Mosflm. We have addressed many bugs and performance issues, and also tidied things up in some of the tasks. If you are using a previous version we strongly recommend that you upgrade. In brief - Improved processing for Pilatus images (both 6M and 2M) Faster processing for large datasets in iMosflm More reliability in indexing, refinement integration Better feedback Easier multi-crystal strategy Available from our website - http://www.mrc-lmb.cam.ac.uk/harry/mosflm == In more detail (see http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/Release_notes for more) - Mosflm == Non-Bragg spots (eg zingers and hot pixels) and ice spots are now automatically removed when forming the standard profiles. Improvements in mosaicity estimation and refinement. Improvements in standard deviation estimates. Improved spot finding parameters for in-house diffraction images and for the very small spots that can be obtained from room temperature (in situ screening) crystals. More robust integration of images with very small spot separation. iMosflm == The colour of the predicted reflections can be changed to improve visibility on weak diffraction images. Improved selection of the correct indexing solution in cases of pseudosymmetry. Scaling and merging now performed with AIMLESS rather than SCALA. Release Notes for iMosflm version 1.0.6 New features The speed of the interface has been much improved when processing a large number of images in the Integration pane. The largest speed-up came from not refreshing the profile displays afresh with every new image integrated. A greatly improved multi-crystal strategy option is available that makes it much simpler to calculate a data collection strategy when multiple crystals or multiple segments from one crystal are required (see below, and also see the new iMosflm tutorial for details). Bad spots identified during processing and whose numbers are plotted during integration can now be displayed in the Image display window. New mosaicity estimation will produce successive plots up to 8 degrees if required. Space group validation has been improved wherever a symbol can also be typed in editable, pull-down lists (Indexing and Strategy panes). The multi-sector, pull-down sectors list used in the Integration pane has been adopted in the Indexing and Cell refinement panes. Initial detector and crystal parameters are saved before refinement and checked that they have not refined to unreasonable values. Users may accept the warnings ( reset the parameters) or ignore them. New items added to the Advanced integration tab of Processing options includes provision for outliers affected by ice rings. The maximum number of images in an integration block has been increased from 20 to 200. The FindHKL function has been placed within the Image display window's toolbar. Smaller rotation increments have been added to the Rotation: setting in the Auto-complete menu in the Strategy pane. The editable 'pie' widget displayed at the bottom of the Strategy pane for any sector can now be adjusted in single degree steps (previously only 5 degree changes were possible). Individual images can now be deleted from the Images pane by selecting them (left-click) and then right-clicking on the selected image. This was previously only available for complete sectors. Scala has been replaced by Aimless as the default scaling program used by the QuickScale command button. Scala can be chosen from the Processing options-Advanced integration tab under the Pointless Aimless/Scala switches. Files containing lists of spots can be read into iMosflm and displayed on the appropriate image. Files can be read from the main Session menu item 'Read spots file...' and from the 'Read spots file...' button (with an open file icon) next to the 'Index' button in the Autoindexing pane. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] iMosflm version 1.0.6 Mosflm version 7.0.8
Where can one find a discussion of the differences between Aimless and Scala? JPK On Mon, Apr 16, 2012 at 8:28 AM, Harry Powell ha...@mrc-lmb.cam.ac.ukwrote: Dear all We are pleased to announce the public release of new versions of iMosflm and Mosflm. We have addressed many bugs and performance issues, and also tidied things up in some of the tasks. If you are using a previous version we strongly recommend that you upgrade. In brief - Improved processing for Pilatus images (both 6M and 2M) Faster processing for large datasets in iMosflm More reliability in indexing, refinement integration Better feedback Easier multi-crystal strategy Available from our website - http://www.mrc-lmb.cam.ac.uk/harry/mosflm == In more detail (see http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/Release_notes for more) - Mosflm == Non-Bragg spots (eg zingers and hot pixels) and ice spots are now automatically removed when forming the standard profiles. Improvements in mosaicity estimation and refinement. Improvements in standard deviation estimates. Improved spot finding parameters for in-house diffraction images and for the very small spots that can be obtained from room temperature (in situ screening) crystals. More robust integration of images with very small spot separation. iMosflm == The colour of the predicted reflections can be changed to improve visibility on weak diffraction images. Improved selection of the correct indexing solution in cases of pseudosymmetry. Scaling and merging now performed with AIMLESS rather than SCALA. Release Notes for iMosflm version 1.0.6 New features The speed of the interface has been much improved when processing a large number of images in the Integration pane. The largest speed-up came from not refreshing the profile displays afresh with every new image integrated. A greatly improved multi-crystal strategy option is available that makes it much simpler to calculate a data collection strategy when multiple crystals or multiple segments from one crystal are required (see below, and also see the new iMosflm tutorial for details). Bad spots identified during processing and whose numbers are plotted during integration can now be displayed in the Image display window. New mosaicity estimation will produce successive plots up to 8 degrees if required. Space group validation has been improved wherever a symbol can also be typed in editable, pull-down lists (Indexing and Strategy panes). The multi-sector, pull-down sectors list used in the Integration pane has been adopted in the Indexing and Cell refinement panes. Initial detector and crystal parameters are saved before refinement and checked that they have not refined to unreasonable values. Users may accept the warnings ( reset the parameters) or ignore them. New items added to the Advanced integration tab of Processing options includes provision for outliers affected by ice rings. The maximum number of images in an integration block has been increased from 20 to 200. The FindHKL function has been placed within the Image display window's toolbar. Smaller rotation increments have been added to the Rotation: setting in the Auto-complete menu in the Strategy pane. The editable 'pie' widget displayed at the bottom of the Strategy pane for any sector can now be adjusted in single degree steps (previously only 5 degree changes were possible). Individual images can now be deleted from the Images pane by selecting them (left-click) and then right-clicking on the selected image. This was previously only available for complete sectors. Scala has been replaced by Aimless as the default scaling program used by the QuickScale command button. Scala can be chosen from the Processing options-Advanced integration tab under the Pointless Aimless/Scala switches. Files containing lists of spots can be read into iMosflm and displayed on the appropriate image. Files can be read from the main Session menu item 'Read spots file...' and from the 'Read spots file...' button (with an open file icon) next to the 'Index' button in the Autoindexing pane. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] iMosflm version 1.0.6 Mosflm version 7.0.8
Aimless is a complete rewrite of Scala, but does essentially the same task. I haven't yet written it up properly, but there is a program document at ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html A rough flow of the program is as follows:- Read file from eg POINTLESS, sort data if necessary (SORTMTZ no longer needed) Initial scale estimates from average intensities First round scaling with small selection of strong reflections, chosen on I/sigI First outlier rejection Optimise the combination of profile-fitted (for weak spots) or summation integration intensities (for strong spots) from MOSFLM First optimisation of sig(I) estimates Main scaling on relatively strong reflections, chosen on normalised intensity E^2 (eg 0.8 E^2 5) Second outlier rejection Final optimisation of sig(I) estimates Final outlier rejection Final statistics Output of merged or unmerged data (MTZ or Scalepack format, or both) Phil On 16 Apr 2012, at 15:42, Jacob Keller wrote: Where can one find a discussion of the differences between Aimless and Scala? JPK On Mon, Apr 16, 2012 at 8:28 AM, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: Dear all We are pleased to announce the public release of new versions of iMosflm and Mosflm. We have addressed many bugs and performance issues, and also tidied things up in some of the tasks. If you are using a previous version we strongly recommend that you upgrade. In brief - Improved processing for Pilatus images (both 6M and 2M) Faster processing for large datasets in iMosflm More reliability in indexing, refinement integration Better feedback Easier multi-crystal strategy Available from our website - http://www.mrc-lmb.cam.ac.uk/harry/mosflm == In more detail (see http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/Release_notes for more) - Mosflm == Non-Bragg spots (eg zingers and hot pixels) and ice spots are now automatically removed when forming the standard profiles. Improvements in mosaicity estimation and refinement. Improvements in standard deviation estimates. Improved spot finding parameters for in-house diffraction images and for the very small spots that can be obtained from room temperature (in situ screening) crystals. More robust integration of images with very small spot separation. iMosflm == The colour of the predicted reflections can be changed to improve visibility on weak diffraction images. Improved selection of the correct indexing solution in cases of pseudosymmetry. Scaling and merging now performed with AIMLESS rather than SCALA. Release Notes for iMosflm version 1.0.6 New features The speed of the interface has been much improved when processing a large number of images in the Integration pane. The largest speed-up came from not refreshing the profile displays afresh with every new image integrated. A greatly improved multi-crystal strategy option is available that makes it much simpler to calculate a data collection strategy when multiple crystals or multiple segments from one crystal are required (see below, and also see the new iMosflm tutorial for details). Bad spots identified during processing and whose numbers are plotted during integration can now be displayed in the Image display window. New mosaicity estimation will produce successive plots up to 8 degrees if required. Space group validation has been improved wherever a symbol can also be typed in editable, pull-down lists (Indexing and Strategy panes). The multi-sector, pull-down sectors list used in the Integration pane has been adopted in the Indexing and Cell refinement panes. Initial detector and crystal parameters are saved before refinement and checked that they have not refined to unreasonable values. Users may accept the warnings ( reset the parameters) or ignore them. New items added to the Advanced integration tab of Processing options includes provision for outliers affected by ice rings. The maximum number of images in an integration block has been increased from 20 to 200. The FindHKL function has been placed within the Image display window's toolbar. Smaller rotation increments have been added to the Rotation: setting in the Auto-complete menu in the Strategy pane. The editable 'pie' widget displayed at the bottom of the Strategy pane for any sector can now be adjusted in single degree steps (previously only 5 degree changes were possible). Individual images can now be deleted from the Images pane by selecting them (left-click) and then right-clicking on the selected image. This was previously only available for complete sectors. Scala has been replaced by Aimless as the default scaling program used by the QuickScale command button. Scala can be chosen from the Processing options-Advanced integration tab under the
