v1.2.0

We are pleased to announce the release mdx-lib version 1.2 to accompany our latest publication:

Meisburger, SP, Case, DA & Ando, N. (2023). Robust total X-ray scattering workflow to study correlated motion of proteins in crystals. Nature Communications (accepted).

Preprint available on bioRxiv: https://doi.org/10.1101/2022.08.22.504832

This major update adds scripts to support a data analysis workflow that includes the GOODVIBES and DISCOBALL methods (manuscript for details).

• New tools to represent atomic scattering factors and ADPs latt.Blob
• New elastic network modelling tools nm.ElasticNetwork_v2, nm.Cell_v2, and nm.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

bioRxiv 2022

Pre-release of version 1.2 to accompany our new manuscript on bioRxiv:

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

This major update adds scripts to support a data analysis workflow that includes the GOODVIBES and DISCOBALL methods (see Meisburger, Case & Ando, 2022 for details).

• New tools to represent atomic scattering factors and ADPs latt.Blob
• New elastic network modelling tools nm.ElasticNetwork_v2, nm.Cell_v2, and nm.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

Nat Comm 2020

This version of mdx-lib was released at the same time as our paper 2020 Nature Communications Paper [1], and it includes scripts to reproduce the data processing and model fitting of lysozyme (P1 space group). There were also extra atomistic modeling libraries not included in the master branch.

[1]: Meisburger, S.P., Case, D.A. & Ando, N. Diffuse X-ray scattering from correlated motions in a protein crystal. Nat Commun 11, 1271 (2020). https://doi.org/10.1038/s41467-020-14933-6

Version 1

The master branch of mdx-lib released at the same time as our 2020 Nature Communications paper [1]. It includes all of the libraries for data processing, but not for atomistic modeling (under development).

[1]: Meisburger, S.P., Case, D.A. & Ando, N. Diffuse X-ray scattering from correlated motions in a protein crystal. Nat Commun 11, 1271 (2020). https://doi.org/10.1038/s41467-020-14933-6