mdx-lib is a general-purpose crystallographic computing library designed for processing and simulating macromolecular diffuse X-ray scattering (MDX).
To see mdx-lib in action, check out mdx-examples.
Meisburger, SP, Case, DA & Ando, N. (2020). Diffuse X-ray scattering from correlated motions in a protein crystal. Nat Commun 11, 1271. https://doi.org/10.1038/s41467-020-14933-6
Meisburger, SP, Case, DA & Ando, N. (2022). Robust total X-ray scattering workflow to study correlated motion of proteins in crystals. bioRxiv 2022.08.22.504832; doi: https://doi.org/10.1101/2022.08.22.504832
Added scripts to support GOODVIBES and DISCOBALL analysis described in Meisburger, Case, & Ando, 2022.
- New tools to represent atomic scattering factors and ADPs
latt.Blob - New elastic network modelling tools
nm.ElasticNetwork_v2,nm.Cell_v2, andnm.LatticeDynamics. These will replace old versions in future release. - Demos moved to separate repository mdx-examples.
- High-level scripts to process maps
proc.script.MapTools,proc.script.GridDesigner,proc.script.MapInterp - Scripts for GOODVIBES analysis:
proc.script.ElasticNetworkTools,proc.script.LatticeDynamicsTools - Scripts for DISCOBALL analysis
proc.script.DeltaPDFTools - Scripts for wrangling crystallographic data files:
proc.script.ImportMTZ,proc.script.ImportPDB
Released at the same time as Meisburger, Case, & Ando, 2020 in a separate branch (natcomm). Includes scripts to reproduce the data processing and model fitting of lysozyme (P1 space group). There were also extra atomistic modeling and normal mode analysis libraries not included in the master branch.
Released at the same time as Meisburger, Case, & Ando, 2020. This more stable version includes all of the libraries for data processing, but not for atomistic modeling or normal mode analysis.
+geom- diffraction geometry and scattering corrections+grid- fractional Miller index grids for voxel integration+io- read and write files+latt- direct and reciprocal lattices, Fourier transforms, electron density of atoms, atomic displacement parameters+model- atomistic modeling, material properties, coherent and incoherent scattering factors+nm- crystalline elastic network modeling and normal mode calculations+proc- algorithms, high-level scripts, and batch processing routines+symm- space groups, symmetry operators, and affine transformations+util- functions and class definitions used by other libraries
The data processing libraries are designed to run on a desktop computer with a large amount of RAM and multiple CPU cores for parallel processing. RAM is needed mostly for processing large datasets or if parallel Batch processing is used. It is recommended to run small-scale tests before scaling up.
The development system was a Mac with 64 GB RAM and 10 cores @ 3 GHz/core.
mdx-lib runs within MATLAB. For full functionality, the following toolboxes should be installed:
- Parallel Processing Toolbox (The Mathworks)
- Statistics and Machine Learning Toolbox (The Mathworks)
The software has been tested on MATLAB version R2021a running on macOS Version 10.14.6 (Mojave). Unix-like paths are assumed throughout (Windows is not tested or supported currently).
Download a release or clone this repository.
Add mdx-lib directory to the MATLAB path. This can be done using the path editor, or for each session by typing (command prompt):
>>> addpath('/<path>/<to>/mdx-lib')CBF decompression is accelerated using MATLAB coder to translate the m-file cbf_decompress.m into c and compile it into a mex file:
+io/@DectrisCBF/private/cbf_decompress_mex.mexmaci64
Since the mex file was compiled on an intel-based Mac, it will only work on similar systems. If using a different OS or architecture, cbf_decompress will need to be re-compiled. The project file is included here:
+io/@DectrisCBF/private/cbf_decompress.prj
Users have also reported the following error:
cbf_decompress_mex.mexmaci64 cannot be opened because the developer cannot be verified
Running this in the terminal should fix the issue (substitute with path to repository on your machine):
sudo xattr -r -d com.apple.quarantine /<path>/<to>/mdx-lib
sudo find /<path>/<to>/mdx-lib -name \*.mexmaci64 -exec spctl --add {} \;We're working on a complete re-implementation in python! Check it out: mdx2