3.5.0 Dec. 14, 2015
3.4.2 Feb. 26, 2014
Full OSX-10.8 and OSX-10.9 support
Auto-saving added
Move image to another project now supported on right-click, useful in case of two crystal conformations
New bug tracker and developer wiki
TTF correction script added for images with a higher tilt then a given value
Internal version control system switched to git
ttfcorfitst removed from Unbend2, as we do not recommend this option at all
dx_automator added
Automated drift-correction
GUI added
Single Particle Processing scripts added, but not ready to use so far
Difference-map functions added
Command line merger
[bug] Beam-tilt refinement now working
[bug] Maximal index in CCP4-script changed in order to achieve high resolution (better than 6A)
Latest version of CTFFIND3 integrated (incl. OMP)
Refine switch now also refines the tilt-geometry
[bug] Resolution plot fixed
[bug] Error on PLTILTK fixed
[bug] Bug in astigmatic handling of CTF fixed
File initialization improved
[bug] Synchronization for .raw.mrc files fixed
[bug] Reference origin resetting works now
Parameters are reset for a new image now
Optimal image import for K2 Summit data
Selection of multiple images with right-click now possible
Possibility to generate non-CTF-corrected map
Removed re-unbending from the standard script list
Added options for tilt-angle range statistics
Included fomstat in 2dx_merge_merge again
Masking both lattices at the same time now possible
[bug] Issue with symmetry p4 in hklsym fixed
PDF translator added
Better sync with backup script
NANs removed from hklsym4-output
mtzdunp now displays all reflections
Non-scroll QComboBox added
refine Defocus now uses only spots up to IQ-4
FOM calculation for symmetry-constraint lattice lines implemented into 2dx_latlinek.for
Lattice line in color now
Tiff translator added
Better spot scan masking functionally
Support for TVIPS-headers
Origtilt output extended
2dx_hklsym3 removed
[bug] Contour plot in p2 now working
Amplitude scaling added
Quality evaluation added (2D and 3D)
Longer image names now supported
MergeIQMAX added
[bug] Unsigned/singed integer issue finally fixed
[bug] TLTPLOT now used correctly
Second lattice determination
Shortcuts to image/merge directory added in 2dx_image/2dx_merge
Shortcut to logbrowser added
Updated change_dylib.sh
More stable Linux support
SBGrid integration
Full build-process done in cmake now
Compilation optimized
SCALIMAMP3d added
Final map exported also as .tif
Sub-volume generation of final map
Use of cpack for Linux package generation
Improved trash functionality
3.4.1 Apr. 9, 2012
PSF in 3D now calculated
tilt geometry variable naming simplified
imagenumber is now also updated, when a default config is used with a wrong image name and number and a new MRC image is found
8×8 binned downsampled nonmasked image now calculated by FFTIR script, for visual tilt geometry from Thon ring fitting.
Changed MRC programs from INTEGER*2 to INTEGER*4
Tilt geometry refinement from MTZ lattice lines can now be done with
GUI-definable parameters
Extended reference maps are displayed in 2dx_merge for each image
Refinement now puts out reference APH files
spotlist is copied from masked to nonmasked name, if needed
allows masking multiple times and with as many vertices as 2dx_boximage can handle
the synchronized property is now also changed in the upper 2dx_master.cfg and we have two save functions, one that synchronizes with the upper config and the other not.
you can now change the threshold for the background and the step size for the contours in the CCP4 map generation
when a parameter in 2dx with the attribute SYNC_WITH_UPPER=yes is saved, it is now also stored in the upper config.
getLattice now favors the vectors that span the smaller angle when reducing them to the shortest even if the one vector is bigger by a delta then the reduced one
allspace now picks the highest symmetry, whose residual is still below the target (=acceptable)
[bug]fixed bug in file selection in the Synchronize Project with Backup script
have the C Shortcut to toggle the thon rings back
Lattice line plot output updated
TAXA display in 2dx_image and 2dx_merge now correctly respects revhk, rot90, etc.
Backup/Restore Databases script created.
CTFTool now allows toggeling of the Thon ring overlay
the Lattice Refine Dialog now shows the selection of a point
changed internal structure of the albumModel to enable more features in the imageAlbum
[bug]fixed bug in display of sheared final maps in Protein Album
Automatic masking in Unbend-II accelerated.
generate_sym_map now works also in p2. A header line was ignored in 2dx_permutate, now fixed.
[bug]bug in 2dx_image script generate-sym-map fixed
Cloning of Image Directory updated.
Synchronization Script created
raw TIFF image handling cleaned up.
FSC-weighted envelope function implemented into Maximum Likelihood code.
cleanup leaves LOGS/*.results in place
ML output map increased, envelope convolution activated.
Script to Repair directory structure added.
Implemented verification of correctly linked 2dx_master.cfg files.
the getLattice script now also allows to refine the tiltgeometry with emtlilt without having to determine the lattice automatically
[bug] SCRATCH_DISK and FFTIR_DISK work even if the original directories do not exist
Inverse Fourier Filtering implemented
color output in distortion plots
[bug]synthetic reference script debugged
only asymmetric unit produced during merging
script to delete images (move to TRASH) updated
2dx_hklsym.for now can do p4212
added parameter refinement script for synthetic unbending
added custom scripts to refine parameters for Unbend I & II first in a coarse grid search over box & mask and then a fine refinement
ctffind3 now works on nonmaskimage, instead of image
Refine Defocus from merged data script
2dx_refine_unbend2 now also allows the refinement of maskb02
2dx_makedirs checks if dirs are empty or not before linking and moves the existing files
2dx_makedirs now creates the symbolic links to the SCRATCH and FFTIR disk
QVAL table is now written as a result of the simultaneous refinement of boxb/boxa and maska/maskb for the Unbending
2dx_image.cfg is now updated appropriately: new paramters are added, changes in parmater properties are updated, and user set parameter properties are kept
SCRATCH_DISK and FFTIR_DISK implemented.
logbrowser becomes the acitve window when popping out of 2dx_image
ztarwin warning only when modus=3D
New Script added to clone an image directory
updates in script Mask Crystal from Polygon
initialization moved into separate script
2dx_maketran.for altered, to prevent gfortran compiler crash
shearing of the generated CCP4 2d map is corrected
[bug]fixed bug #32: update version text. Plus the http get request is now done the qt4 way.
verbose logging of merging statistics in 2dx_origtiltk implemented. An additional file 2dx_origtiltk-reflections.log is created now.
[bug]bug in 2dx_latlinek resolved, where ZSTG was not initialized (reported by William Nicholson)
progressStamps are visible again
changes to get the resources path
IS_WRONG is now depicted by the background color
Automatic Scaling to INTEGER*2 0…16000 implemented
Now also reads *.tiff in addition to *.tif
[bug]bug removed that led to crash when 2dx_image.cfg was outdated.
Delete Image as script added.
PLTILTK in 2dx_merge included.
3.3.0 Dec. 24, 2010
[Bug] 3D reference values from lattice lines are now correctly sorted, so that the creation of synthetic unbending references via MAKETRAN now works.
[Bug] Fixed a bug in synthetic unbending when using TTF.
Added a script option in 2dx_image for the tilt geometry refinement from defocus gradient.
2dx_merge now plots FOM-Symbol plot for non-tilted merged data.
2dx_merge now creates correct symbolic links for the configuration files 2dx_master.cfg upon initialization of a new project. These links are needed for correct synchronization of global parameters (e.g. synchronization of the crystal symmetry).
Added the configuration file 2dx_merge-user.cfg into the user's home directory/.2dx, which stores user settings for 2dx_merge. It is also used by the file browser to navigate to the last used project directory.
[Bug] 2dx_image becomes now the active window even when its called from 2dx_merge.
CCP4 can now also be located in /Applications on MAC
OS X.
The local database 2dx_merge.cfg is now updated, when new parameters are added to the master configuration file /usr/local/2dx/kernel/config/2dx_master.cfg.
Added a new parameter attribute ISWRONG, which when set to YES visualizes the specified values in the
GUI in grey. This depicts that these values should be altered before processing. By editing them they become black on white, and ISWRONG is set to NO. This allows to have parameters prefilled with default values that are technically functional, but still wrong. For example, the default setting for defocus is 5000.0, but the exact value still has to determined. The defocus entry of 5000.0 is therefore initially labeled as ISWRONG.
The variable attribute GLOBAL in the CShell scripst has been replaced with DISPLAY to make its functionality more clear. Scripts containing the attribute GLOBAL will still run.
Updated the merging scripts so that Maximum Likelihood (ML) processing results from 2dx_image can also be used for merging. For this purpose, a new parameter ML_use_for_merging has been introduced, which allows to decide, if a ML result should be used for merging, or if the Unbending result should instead from this image be used for merging.
[Bug] Fixed a bug in the ML code, which resulted in the Amplitude and Phase data to be written out with 180deg phase shift with respect to the Unbending results.
Added a feature that checks if the symmetry parameter setting for ML processing is following the same space group symmetry as otherwise choosen for the project.
[Bug] Fixed a bug in the ML code, which resulted in the Amplitude and Phase data to be written out without the initial image idenfier number. This prevented this file from being able to be included in the merging.
Added a parameter mask_reset_reflocation that allows to decide, if during masking and optionally cropping of the crystal area the reference location should be reset to the new center of the crystal, or if it should remain in the old position.