Recent Releases of xtrapol8
xtrapol8 - Release Xtrapol8 v1.2.9
Improvements: - Standalone versions to recalculate the difference-map and distance analysis are easier to use: - input.phil file - information extracted from Xtrapol8_out.phil
New features: - new keyword to define the scattering table, only accessible via command line: - scatteringtable = *ngaussian wk1995 it1992 electron neutron
- Python
Published by ElkeDeZitter about 1 year ago
xtrapol8 - Release Xtrapol8 v1.2.8
Fixes: - Problems with ddm: the problem is solved with Pandas which is supported from phenix v.1.20 onwards - Problem with output directory in standalone version of difference map analysis. - The default output directory is now called "Differencemap_analysis" instead of the current working directory
Improvements: - GUI: - map explorer parameters are always shown, not only when in expert mode - scaling B-factor moved to expert mode - new features have been incorporated - names have been updated - update of the refinement tab according to the new refinement program combinations
New features: - --help, -h and --version - Refinement can now be carried out with different program combinations: - Use the following keywords: - refinement.reciprocalspace = *phenix.refine refmac5 - refinement.realspace = *phenix.realspacerefine coot - the keyword refinement.userefmacinsteadofphenix still can be used and will be interpreted as - refinement.reciprocalspace=refmac - refinement.realspace=coot - Negative and missing ESFAs: - the arguments "absoluteandfill" and "absolutenofill": - "absolute" means that the absolute values of the ESFAs will taken, independent of their calculated sign - "fill" or "no_fill" has influence on the automatic filling of missing reflections for the calculations of electron density maps.
- Python
Published by ElkeDeZitter over 1 year ago
xtrapol8 - Release Xtrapol8 v1.2.7
Fixes: - bug in map-explorer analysis summeddifferencepeaks figure
- Python
Published by ElkeDeZitter over 1 year ago
xtrapol8 - Release Xtrapol8 v1.2.6
Fixes: - Extraction of Phenix and CCP4 version: - bug solved when the version cannot be extracted from the installation path - refiner.py: - Phenix version now extacted as in Fextr.py - some Phenix v1.21 keywords are now correctly recognised - uses the versioning as in Fextr.py
- Python
Published by ElkeDeZitter over 1 year ago
xtrapol8 - Release Xtrapol8 v1.2.5
Fixes: - map-explorer: - should not bug anymore when no peaks are selected from the FoFo map - refiner.py: - bugs with random tag from log file solved - variables not called anymore before their generation - refinement with phenix.refine v1.21: - map-shapening will generate non-standard columns in the output mtz file. Subsequent real-space refinement can now continue because column labels will be guessed (mostly correctly; see below)
Improvements: - real-space refinement with phenix.realspacerefine: - check if column labels in mtz file exists before launching real space refinement - a guess as which column labels to use is done if the exact column label cannot be found
- Python
Published by ElkeDeZitter almost 2 years ago
xtrapol8 - Xtrapol8 v1.2.4
Fixes: * Data type can be altered in GUI for mtz and gif files
- Python
Published by ElkeDeZitter almost 2 years ago
xtrapol8 - Release Xtrapol8 v1.2.3
Improvements: * default range of occupancy values is set to more sensible values * improved documentation * easier version handling * report version of phenix and ccp4 * plots: labels are more consistent between each other
Fixes: * log files gets a temporarily tag to avoid that multiple jobs want to write in the same log file
New features: * compatibility with phenix v 1.21 (at least for Macos)
- Python
Published by ElkeDeZitter almost 2 years ago
xtrapol8 - Release Xtrapol8 v 1.2.1
Fixes: * density modification with dm: * the density modified map is read in correctly for real space refinement * the density modified map is also opened via the COOT script
- Python
Published by ElkeDeZitter over 2 years ago
xtrapol8 - Release Xtrapol8 v 1.2.0
New features: * scaling: * resolution boundaries for scaling only can now be added * occupancy estimation: * new keyword “mapexplorer.occupancyestimation”: * allows the user to directly select the main method for occupancy determination. This makes the "mapexplorer.useoccupancyfromdistanceanalysis” keyword obsolete * negative and missing ESFAs: * the arguments “keepandfill” and “keepnofill”: * replacing the former "fillmissing" and “nofill” * "keep" means that the negatives will be kept negative. "fill" or "nofill" has influence on the automatic filling of missing reflections for the calculations of electron density maps. * the "keepnofill" maps are automatically added to the output subfolders
Improvements: * dm: * default parameters changed to OMIT and 3 cycles * electron density maps: * xplor maps are no longer written, strongly reducing the size of the Xtrapol8 output folder
- Python
Published by ElkeDeZitter over 2 years ago
xtrapol8 - Release Xtrapol8 v 1.1.0
Improvements: - ddm: - updated to show gap for missing residues - standalone version - alpha determination via difference map analysis: - generation of a mask based on the FoFo map (z-scored peaks) - plot based on the Fextr-Fcalc maps directly instead of the list of peak heights and integrated values - addition of the Pearson correlation coefficient between FoFo and Fextr-Fcalc - output directory as additional argument in the standalone version - compatibility of ccp4 and xplor maps
- Python
Published by ElkeDeZitter about 3 years ago
xtrapol8 - Xtrapol8 version 1.0.0
This is the first Xtrapol8 release. More information concerning Xtrapol8 can be found in De Zitter, et al., https://www.nature.com/articles/s42003-022-03575-7
- Python
Published by ElkeDeZitter over 3 years ago