Dear All:

 

We announce the release of a new version of our program package SIMPLE (v2.5) for single-particle cryo-EM ab initio 3D reconstruction (web: simplecryoem.com)

 

New features include:

 

* A new DDD movie pre-processing program that implements motion correction based the same principal strategy as Grigorieff's Unblur. There are two important differences: automatic weighting of the frames using a correlation-based M-estimator and stochastic continuous optimisation of the shift parameters. This enables analysis of movies with severe pathologies due to radiation damage or extreme drift.

 

* A new program for DDD movie pre-processing of tomographic tilt-series.

 

* Improved simultaneous 2D alignment and clustering with PRIME2D using a hybrid extremal/stochastic hill-climbing search approach, Wiener restoration-based CTF correction and acceleration of the search using Hadamard projection matching. It is now possible to generate a sub-nanometer resolution ab initio 3D reconstruction from class averages obtained with PRIME2D in a about 10 minutes on a laptop (MacBook Pro mid 2015, 2.8 GHz Intel i7, four physical cores).

 

* Improved ab initio 3D reconstruction from class averages using stochastic neighbourhood hill-climbing for initialisation of the 3D orientation search, improving the success rate from around 40% to 90-100% for more challenging starting model generation problems, executed with the new program ini3D_from_cavgs.

 

* Serial CPU code optimisation through data re-organisation and pipelining.

 

* Improved parallel CPU performance through load balancing as well as data and algorithm re-organisation. It is now possible to process data sets of realistic size on laptops or lightweight workstations that cost less than 2,000 USD.

 

* High-level workflows for 2D analysis and initial 3D model generation that automates initialisation, updates search parameters automatically and dynamically down-scales the images for improved performance.

 

If you need help installing SIMPLE, optimising its execution for your computer architecture or experience any problems or bugs please use the contact form on the webpage (www.simplecryoem.com/contact.html) to file a help ticket. We will endeavour to respond within two days.

 

Happy image processing!

 

The SIMPLE team:

 

Cyril F Reboul

Michael Eager

Dominika & Hans Elmlund