Roodmus is computational toolkit that allows sourcing conformational heterogeneity of biological macromolecules from atomistic molecular dynamics simulations to generate realistic, synthetic cryo-EM datasets, and parsing information about the exact pose and conformation of each particle along the entire reconstruction workflow. This allows the results of heterogeneous reconstruction algorithms and the effect of experimental factors such as radiation damage, preferred orientations or electron optical aberrations on their outcome, to be systematically investigated by comparison to ground truth information.


Availability: roodmus is freely available under the GPL licence. For more information as well as download/installation instructions please visit the repository. A detailed description of use, best practices and analysis tools are available on the README and scripts directory.

roodmus was developed in collaboration with Joel Greer and Tom Burnely at CCP-EM.

If roodmus is useful for you work please consider citing the original reference. If you utilize the CCP-EM implementation of roodmus please also credit the CCP-EM project.
_{Joosten, Greer et al., BioRxiv 6:e27131 (2024)     | doi |}  

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 |}  

PySerialEM is a small Python library to read/write and manipulate SerialEM navigator (.nav) files, or to process (e.g. montage) SerialEM grid maps.

Availability: PySerialEM is freely available under the BSD licence. General instructions can be found here.

NEW: See here for Stef’s demo on grid montaging.

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 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 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 ParaSurf^TM package by Cepos InSilico. It requires a semi-empiricial molecular orbital program such as VAMP, EMPIRE^TM or Mopac6.

_{J Mol Model 14:547-558 (2008)     | doi |}  
Availability: A restricted version of ParaSurf^TM and EMPIRE^TM is freely available for bona fide academic users (register).

* Tools & scripts for model building and refinement