About LocScale 2.0

LocScale 2.0 has been developed by Alok Bharadwaj and Arjen Jakobi at the Kavli Institute of Nanoscience Delft, with contributions by Reinier de Bruijn to the development of EMmerNet.

Credits

LoScale 2.0 is facilitated by a number of open-source projects.

Projects used in LocScale

EMmer: Python library for electron microscopy map and model manipulations. [3-Clause BSD license]
FDRthresholding: Tool for FDR-based density thresholding. [3-Clause BSD license]
EMDA: Electron Microscopy Data Analytical Toolkit. [MPL2.0 license]
Servalcat: Structure refinement and validation for crystallography and SPA. [MPL2.0 license]
mrcfile: MRC file I/O. [3-Clause BSD license]

LocScale also makes use of REFMAC5. Refmac is distributed as part of CCP-EM.

We acknowledge the use of computational resources of the DelftBlue supercomputer, provided by Delft High Performance Computing Centre.

References

If you found LocScale-2.0 useful for your research, please consider citing it:

A.J. Jakobi, M. Wilmanns and C. Sachse, Model-based local density sharpening of cryo-EM maps, eLife 6: e27131 (2017).
A. Bharadwaj and A.J. Jakobi, Electron scattering properties and their use in cryo-EM map sharpening, Faraday Discussions 240, 168-183 (2022)

A preprint describing LocScale 2.0 is in preparation.

Bugs and questions

For bug reports please use the LocScale issue tracker.