This is a directory to scientific software from our lab that is freely available to the academic community. Most of our developments are concerned with postprocessing of cryo-EM maps and atomic model refinement using cryo-EM data. Please visit the individual pages for more details if you are interested. You can also find a collection of potentially useful jiffys and tools for cryo-EM model building.

All projects are hosted by our group respository on Gitlab.


LocScale

Schematic illustration of the LocScale map sharpening
Schematic illustration of the LocScale map sharpening

LocScale is a reference-based local amplitude scaling tool using prior model information to improve contrast of cryo-EM density maps. It can be helpful in the common case of resolution variation in the 3D reconstruction and it can be used as an alternative to other commonly applied map sharpening methods.

Availability:

LocScale is freely available under the BSD licence. For more information as well as download/installation instructions please visit the Gitlab repository. Tutorial files and a detailed description of use and best practices are available on the Wiki pages.

NEW: An accelerated and GUI-supported version of LocScale has now been integrated into the CCP-EM suite and is distributed with the latest release v1.2.0.

If LocScale is useful for you work please consider citing the original reference. If you utilize the CCP-EM implementation of LocScale please also credit the CCP-EM project.

Jakobi et al., eLife 6:e27131 (2017)     | doi |  
Burnley et al., Acta Cryst. D73:469-477 (2017)     | doi |  



instamatic

instamatic: Automated electron diffraction data acqusition
instamatic: Automated electron diffraction data acqusition

instamatic is a tool for automated acquisition of electron diffraction data on transmission electron microscopes. It provides a Python library for microscope control via the COM interface provided by the TEM manufacturer, with bindings for JEOL/TFS microscopes and interfaces to Gatan/Timepix/TVIPS cameras. Routines have been implemented for collecting serial electron diffraction (serialED), continuous rotation electron diffraction (cRED), and stepwise rotation electron diffraction (RED) data.

instamatic is being developed by Stef Smeets.

Availability:

instamatic is distributed as a portable stand-alone release that includes all required libraries. The most up-to-date version of the code (including bugs!) is available from this repository.

If instamatic is useful for your work please consider citing one of the references below and/or reference the source code.

Smeets et al., Zenodo (2018)     | doi |  
Cichocka et al., J. Appl. Cryst. 51:1652–1661 (2018)     | doi |  



rsref

rsref is a scripted modular workflow for the refinement of atomic models against high-resolution cryo-EM density maps. It is a not a standalone refinement software, but rather provides a set of tools for model and/or map manipulation, refinement protocols, the analysis of the refinement cycles and validation of the resulting coordinate models.

rsref makes use of the libraries from the cctbx project.

Availability:

rsref is an ongoing development and not officially released. If you are fine with limited support, please see the Wiki pages for dowload and usage instructions and tutorial.

If rsref is useful for you work please acknowledge the cctbx project (doi).


Primary references:
Nature 528:231-236 (2015)       | doi |  
FEBS J 283:2811–2819 (2016)   | doi |  



ParaFrag

Local electron affinity mapped onto the isodensity surface of a caprolactam derivative inhibitor
Local electron affinity mapped onto the isodensity surface of a caprolactam derivative inhibitor

ParaFrag is a method for atom-independent bioisoster searching of molecular fragments. The approach is based on similarity comparison of local surface property extrema calculated on isodensity surfaces by semi-empirical molecular orbital methods. The method has been applied for applications in drug design (scaffold hopping). Please see here for additional information.

ParaFrag has been developed together with Timothy Clark (Computer Chemistry Center, Erlangen) and Harald Mauser (F.Hoffmann-La Roche, Basel).

ParaFrag is distributed as part of the ParaSurfTM package by Cepos InSilico. It requires a semi-empiricial molecular orbital program such as VAMP, EMPIRETM or Mopac6.

J Mol Model 14:547-558 (2008)     | doi |  

Availability

A restricted version of ParaSurfTM and EMPIRETM is freely available for bona fide academic users (register).



Script collections

  • Collection of tools & scripts for model building and refinement - link