<div dir="ltr"><div>Dear All:<br></div><div> </div><div>We announce the release of a new version of our program package SIMPLE (v2.5) for single-particle cryo-EM <i>ab initio</i> 3D reconstruction (web: <a href="http://simplecryoem.com">simplecryoem.com</a>)</div><div> </div><div>New features include:</div><div> </div><div>* 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.</div><div> </div><div>* A new program for DDD movie pre-processing of tomographic tilt-series.</div><div> </div><div>* 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 <i>ab initio</i> 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).</div><div> </div><div>* Improved <i>ab initio</i> 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.</div><div> </div><div>* Serial CPU code optimisation through data re-organisation and pipelining.</div><div> </div><div>* 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.</div><div> </div><div>* 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.</div><div> </div><div>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 (<a href="http://www.simplecryoem.com/contact.html">www.simplecryoem.com/contact.html</a>) to file a help ticket. We will endeavour to respond within two days.</div><div> </div><div>Happy image processing!</div><div> </div><div>The SIMPLE team:</div><div> </div><div>Cyril F Reboul</div><div>Michael Eager</div><div>Dominika & Hans Elmlund</div><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><p style="font-size:12pt;margin-bottom:0px;margin-top:24px;line-height:24px;font-family:"times new roman",serif;color:rgb(96,102,109)"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;line-height:normal">-- </span><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;line-height:normal"></p><div style="line-height:normal;font-size:small"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font face="arial narrow, sans-serif"><span style="font-size:12.8px"><b>HANS ELMLUND PhD </b> </span><br></font></div><div><font face="arial narrow, sans-serif">Associate Professor</font></div><div dir="ltr"><font face="arial narrow, sans-serif"><br></font></div><div dir="ltr"><font face="arial narrow, sans-serif"><b>ARC Centre of Excellence for Advanced Molecular Imaging</b></font></div><div><font face="arial narrow, sans-serif"><b>Dept. of Biochemistry and Molecular Biology</b></font></div><div dir="ltr"><font face="arial narrow, sans-serif">Monash University</font></div><div dir="ltr"><font face="arial narrow, sans-serif">Room 228, Level 2, Building 77, Clayton Campus</font></div><div dir="ltr"><div><font face="arial narrow, sans-serif">23 Innovation Walk</font></div><div><font face="arial narrow, sans-serif">Clayton VIC 3800 </font></div><div dir="ltr"><font face="arial narrow, sans-serif">Australia</font></div></div><div dir="ltr"><font face="arial narrow, sans-serif"><br></font></div><div dir="ltr"><font face="arial narrow, sans-serif">T: +61 399029310 </font></div><div dir="ltr"><font face="arial narrow, sans-serif">M: +61 (0)45271213</font></div><div dir="ltr"><font face="arial narrow, sans-serif">E: <a href="mailto:hans.elmlund@monash.edu" style="color:rgb(17,85,204)" target="_blank">hans.elmlund@monash.edu</a></font></div><div dir="ltr"><a href="http://simplecryoem.com/" style="font-size:12.8px" target="_blank">simplecryoem.com</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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