BioXTAS RAW News

I'm pleased to announce the release of RAW version 2.4.1. This is a bug fix release. It also fixes compatibility issues with ATSAS 4.1.3. The other change of note is that it introduces a new workspace save format. Workspaces now save as .hdf5 files. This fixes compatibility issues that could occur with old-style workspaces saved from different versions of RAW. It also results in significantly smaller file sizes for workspaces with series in them. Old style workspace files (.wsp) can still be loaded, but all new workspaces will be saved as .hdf5 files, and those will require RAW version 2.4.1 or newer to load.... read more

I'm pleased to announce the release of RAW version 2.4.0. This release has a new Multi-series analysis module that can be used to carry out profile by profile averaging, subtraction, and manipulation such as q binning and truncation on multiple series at once. This is useful for example to carry out point-by-point buffer subtraction for an IEC-SAXS elution where you measured a matching buffer gradient or to carry out more complicated analysis of time-resolved SAXS data. Further details can be found here: Multi-series analysis tutorial.... read more

I'm pleased to announce the release of RAW version 2.3.1. This is a bug fix release that fixes several compatibility issues and other known bugs in RAW. The main update for this release is a new Windows 11 specific installer that will hopefully fix issues with the existing Windows installer not working for some Windows 11 computers.

Other notes:

• This will be the last version of RAW to have a pre-built installer that supports Windows 10.
• The Linux installer now supports a minimum version of Ubuntu 22.04/Debian 12.
• The MacOS installer now supports a minimum version of MacOS 13 (Ventura).... read more

I'm pleased to announce the release of RAW version 2.3.0. Significant changes include:

• Added the DENSS IFT method, which provides an open-source alternative to GNOM for IFTs with an adjustable Dmax parameter (unlike BIFT, which has a fixed, automatically determined, Dmax).
• Added the DENSS PDB2SAS method, which provides an open-source alternative to CRYSOL for predicting scattering profiles from models.
• High DPI support for plots on MacOS (requires matplotlib >= 3.9).
• High DPI support for the entire program on Windows (requires matplotlib >= 3.9).
• Compatibility updates for ATSAS 4.0.... read more

I'm pleased to announce the release of RAW version 2.2.2.

Installation links are available here:
https://bioxtas-raw.readthedocs.io/en/latest/install.html

This version is mostly minor bug fixes. Of note is that it includes the citation for the new RAW paper: BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis. J. B. Hopkins. Journal of Applied Crystallography (2024). 57, 194-208. DOI: 10.1107/S1600576723011019. Available: https://doi.org/10.1107/S1600576723011019... read more

The RAW team is pleased to announce the release of RAW version 2.2.1. This version contains a single bug fix:

• Fixed a bug that prevented some calibration and masking operations from being used.

Because this bug prevented the use of major features it warranted a quick fix.

All changes:

• Fixed a bug that prevented some calibration and masking operations from being used when running with newer versions of matplotlib (including the prebuilt installers).

The RAW team is pleased to announce the release of RAW version 2.2.0.

Installation links are available here:
https://bioxtas-raw.readthedocs.io/en/latest/install.html

Significant changes include:

• Integration of CRYSOL into the GUI and API. You can now generate theoretical profiles by simply plotting a .pdb or .cif file, or you can open the CRYSOL analysis window and adjust the settings and fit the model to experimental data (https://bioxtas-raw.readthedocs.io/en/latest/tutorial/s2_crysol.html).
• A new profile comparison window that provides residual and ratio plots, as well as a heatmap of the probability profiles are the same based on the selected similarity test (https://bioxtas-raw.readthedocs.io/en/latest/tutorial/s1_similarity.html).
• Faster calculation of SVD and forward and backward EFA plots
• Improved PDF report with text wrapping in columns so that tables can't extend off the edge of the page and vector graphics plots.... read more

In order to take advantage of the more robust web-based collaboration tools, particularly in terms of pull requests and merging, I've migrated the source code to github:
https://github.com/jbhopkins/bioxtasraw

The git on sourceforge will no longer be updated, however we will continue using sourceforge for releases.

• Jesse

The RAW team is pleased to announce the release of RAW version 2.1.4. Significant changes include:

• Compatibility with ATSAS 3.1.0

Due to some changes in ATSAS, you may notice some differences in the associated RAW tools:

• SUPCOMB has been replaced with CIFSUP.
• DAMCLUST is now included in DAMAVER, and so is no longer an option in the DAMMIF/N GUI.
• SASRES is not included in DAMAVER 3.1.0 output, but is in 3.1.1.
• Output formats for DAMMIF/N are now .cif files.
• DAMAVER is now multi-core. This greatly improves the speed, but as of now we don't see any way to restrict the number of cores it uses, so the number of processors specification in the DAMMIF/N window only applies to the reconstructions, not the averaging.
• Clustering results from DAMAVER no longer include average cluster deviation or distance between clusters, so that is not reported. Eventually the GUI may be updated to remove those values, but since we suspect many people will keep using the older version of DAMCLUST for a while we will leave those fields in the GUI for now.
• Note that the tutorials have been updated for ATSAS 3.1, but if you have an older version of ATSAS installed you will see the options appropriate for that version.... read more

The RAW team is pleased to announce the release of RAW version 2.1.3. This version contains a single bug fix:

• Fixed a bug that could prevent data from loading into RAW after the RAW window was dragged between two monitors.

It's not clear how prevalent this bug was, but given the potential severity it warranted a quick fix/release.

NOTE: As of now, RAW is not compatible with ATSAS 3.1.0, which is currently available for download as a pre-release. This is because ATSAS 3.1.0 is currently missing several important programs, such as some of the DAMAVER set of tools, so we can't test against that. Once ATSAS 3.1.0 is officially released we will update RAW to support it. The same may apply to the 3.2.0 pre-release, we haven't been able to test that yet.... read more

The RAW team is pleased to announce the release of RAW version 2.1.2. This version contains mostly minor bug fixes. Significant changes include:

• Added a prebuilt version for arm64 chips on MacOS (Apple Silicon).
• Removed Windows 7 and 8 support form the prebuilt version for Windows.
• Added support for Eiger2 images from BioCAT.
• Improved handling of multi-image files.
• Adds a new dependency on mmcif_pdbx to read mmcif files.... read more

The RAW team is pleased to announce the release of RAW version 2.1.1. The
major change in this version is:

• Fixed a serious bug that would cause RAW to crash on Ubuntu.

There are also several other small bug fixes and new features.

All changes:

• Fixed a serious bug that would cause RAW to crash on Ubuntu (and possibly other OSes).
• Fixed a bug where closing the Guinier window before autorg finished would result in an error.
• Fixed a bug that could cause an error if the auto_dmax function failed to return a result.
• Fixed a bug where using simple concentration regularizers would fail.
• Fixed a bug where caching of certain compiled functions wasn't working, leading to them having to be compiled every time RAW was opened.
• Tweaked when functions are compiled to try to speed up the user experience, particularly when opening the Guinier window, and either IFT window.
• Improved the speed of BIFT on Linux and Windows.
• Fixed an issue where RAW wouldn't work with matplotlib>=3.4.1.
• Fixed an issue where available fonts weren't properly displayed in the prebuilt versions.
• In the RAW API, BIFT now defaults to single processor (should be faster), and you can specify the number of processors to use if you use it in multiprocessor mode.

The RAW team is pleased to announce the release of RAW version 2.1.0. This version sees the release of two major new features:

• Analysis reports on your data can now be saved as PDFs.
• The release of a GUI for the REGALS technique, a new way to deconvolve overlapping LC-SAXS peaks. REGALS can be thought of as an extension and enhancement of EFA for other types of SAXS data, such as ion exchange chromatography, titration series, and time resolved SAXS. You can read more about REGALS here.... read more

The RAW team is pleased to announce the release of RAW version 2.0.3. While this is only a point release, we are releasing a major new feature for RAW. There are only minor modifications to the RAW GUI, but we are releasing an entirely new RAW API. This means that RAW can now be imported as a python package and you can call RAW functions in your own scripts. The API is fully documented, and the documentation plus install instructions and some examples are available on the RAW website.... read more

The RAW team is pleased to announce the release of RAW version 2.0.2. The
major change in this version is:

• Fixed a bug where SAXSLAB images couldn't be loaded.

There are also a number of other small bug fixes and new features.

All changes:

• Can now load .dat files from WAXSiS, .dat files that are comma separated.
• Fixed a bug where the Vc integrated intensity plot was blank if the scattering profile had saved M.W. results.
• Improved rebinning functions, particularly the log binning function.
• Fixed a bug where error wasn't interpolated properly when interpolating a profile.
• Fixed a bug where pixel size from header bindings was in the wrong units.
• Fixed a bug where series type could get lost in certain operations.
• Fixed a bug where centering and enantiomorph selection options were ignored in the DENSS alignment panel.
• Fixed a bug where series buffer range finding was scaling profiles before testing for similarity.
• Fixed a bug where SAXSLAB images failed to load with pillow version 7.
• Fixed a bug where SAXSLAB images failed to radially average.
• Fixed a bug where images wouldn't load if there was no beamstop mask.
• Fixed a bug that could result in calculated data not displaying on the series plot.
• Fixed a bug where series saved as .hdf5 with EFA analysis would fail to open the EFA window when reloaded.
• Fixed a bug where datgnom couldn't be run on truncated profiles.
• Fixed a bug where opening the advanced settings window from the GNOM window didn't properly update changed settings in the GNOM window.
• Fixed a bug where .hdf5 files couldn't be plotted by dragging and dropping or using the 'Plot Series' button.
• Fixed a bug where running a dammin refine with too long a filename would fail (previously thought to be fixed in 2.0.0).
• Fixed a bug that could prevent DENSS from starting on Windows and Linux.
• Fixed a bug that could prevent auto determination of number of components in EFA.

The RAW team is pleased to announce the release of RAW version 2.0.1. This version fixes several serious bugs in the previous version, including:

• A bug where some of the M.W. calculations failed for profiles with a maximum q value greater than 0.5.
• A bug where the standalone DENSS alignment window failed to run on Windows and Linux.
• A bug where killing the prebuilt version of RAW on Linux would fail to delete temporary files, which could lead to the /tmp partition filling up.... read more

I'm happy to announce that I've created a new set of RAW tutorial videos, which are now available on youtube:
https://www.youtube.com/playlist?list=PLm39Taum4df4alFnacOOr1RWgylwiTWED

There is now a tutorial video for each section of the RAW Tutorial, and those videos are linked in the appropriate tutorial sections on the raw website (https://bioxtas-raw.readthedocs.io/en/latest/index.html).

You can also find the tutorial videos linked in the videos section on the RAW website.... read more

The RAW team is pleased to announce the release of RAW version 2.0.0. This version
brings a number of exciting changes, including:

• Python 3 compatibility!
• Conversion to pyFAI for radial integration
• A .deb prebuilt installer for Debian/Ubuntu
• A new series save format, .hdf5, that can be easily read by other programs. This new format is also ~50-70% smaller than the previous format.
• New information windows above the control panel to display all your analysis
• Ability to align DENSS and DAMMIF/N outputs to PDB files
• Works with ATSAS 3 on all platforms
• New Series adjustment panel that lets you adjust the scale, offset, and q range for all profiles in a series easily.... read more

The RAW team is pleased to announce the release of RAW version 1.6.4. This version adds in a new header type for the MacCHESS SAXS beamline Eiger 4M detector. There are also a few other minor bug fixes.

All changes:

• Fixed a bug where negative values for error would cause points to not be read from .dat files.
• Fixed a bug where the BIFT window wouldn't open if the profile and n min or n max for the q vector set to other than 0 and the length of the q vector.
• Fixed a bug where looking for bind list keywords that don't exist in the RAW settings would prevent a file from loading.
• Fixed a bug where damaver didn't run with symmetry even if dammif did.
• Added a name to the dock/menu bar icon.
• Fixed a bug with moving masks.
• Added CHESS EIGER 4M to counter file reader options.
• Fixed type-casting issues for max/min in polygonmasking that caused errors on some older systems.

The RAW team is pleased to announce the release of RAW version 1.6.3. This version fixes a critical bug where when averaging detected different files, regardless of user choice it would always average all files (selecting just similar files didn't work). There are also a few other minor bug fixes.

All changes:

• Fixed a bug where if you averaged, subtracted, or merged two items with analysis done on them, you could end up with partial analysis info in the resulting file that would cause errors opening analysis windows.
• Fixed a critical bug where when averaging detected different files, regardless of user choice it would always average all files (selecting just similar files didn't work).
• Fixed a bug where the MW window wouldn't open if the Guinier fit hadn't been done.
• Fixed a (Debian specific?) bug where wx.CallAfter used with wx.MessageBox wasn't threadsafe and could cause RAW to crash (use wx.MessageDialog).

The RAW team is pleased to announce the release of RAW version 1.6.2. This version fixes several critical bugs that could prevent DENSS from running. There are no other changes.

The RAW team is pleased to announce the release of RAW version 1.6.1. This version contains numerous small bug fixes and improvements, particularly for the new series analysis methods released in version 1.6.0.

We anticipate this will be the last release before RAW version 2.0, which will be our first python 3 compatible release. We're aiming to release version 2.0 sometime around the end of the year.... read more

The RAW team is pleased to announce the release of RAW version 1.6.0. This version contains several major changes:

• Completely new and improved SEC-SAXS processing, including new automated buffer and sample region selection and baseline correction. There are also significant speed improvements for SEC-SAXS processing, in addition to the new features.
• Completely redone BIFT, which fixes several bugs (both minor and major), and adds Monte Carlo error estimation and extrapolation fit of data to I(0).
• RAW now preserves matching metadata across processes like averaging and subtraction. Metadata is now saved with keywords compatible with the SASBDB to make uploading there easier for users. Users can now also provide arbitrary metadata during data reduction.
• All new icons which are compatible with retina displays, including changing out the check mark for showing/hiding data on plots for an eye, which we hope will be more intuitive.
• RAW now loads the last used config, rather than the last saved config, when it starts up.
• Any analysis window (Guinier, MW, GNOM, etc) can now be opened more than once, allowing easy comparison or side-by-side processing of data sets.... read more

The RAW team is pleased to announce the release of RAW version 1.5.2. The only change is this version is a modification to how BioCAT header files are read in, to accommodate a new header file format at that beamline. Look for lots of new features, including completely revised Series data analysis, in the next release!

The RAW team is pleased to announce the release of RAW version 1.5.1. This version contains several small bug fixes. Normally we might wait to release these until more major changes had happened, but there is a workshop using RAW soon and we wanted these bugs fixed before then. Significant issues that have been eliminated:

• An issue where the electron density output from DENSS could fail to load into pymol correctly because the default scaling was too small (still loaded into Chimera fine). Strictly speaking I think this is a workaround for a bug in pymol …
• Several bugs with running GNOM, including using data with minimal sampling (<100 points).
• Fixed a bug where the .app package for Mac wasn’t displaying natively on retina displays, so the text was fuzzy.... read more