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<div class="">We are pleased to announce a new release of the joint distribution of EMAN2/SPHIRE/SPARX. This represents the final release before we transition to Python 3 (the end of the year when Python2 becomes deprecated). </div>
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<div class="">see either:</div>
<div class=""><a href="http://eman2.org" class="">http://eman2.org</a></div>
<div class="">or</div>
<div class=""><a href="http://sphire.mpg.de/wiki/doku.php?id=downloads:sphire_1_3" class="">http://sphire.mpg.de/wiki/doku.php?id=downloads:sphire_1_3</a></div>
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<div class="">As always, all 3 software packages are part of a single installation. Each package uses a unique command prefix:</div>
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<li class="">EMAN2: e2</li><li class="">SPHIRE: sp</li><li class="">SPARX: sx</li></ul>
<h4 class="">Version changes</h4>
<p class=""><u class="">EMAN2 major changes:</u></p>
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<li class="">PPPT (per particle per tilt) Subtomogram averaging:
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<li class="">Automatic CTF based handedness checking for tomograms</li><li class="">focused refinement <a href="https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_more#Focused_refinement" class="">https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_more#Focused_refinement</a></li><li class="">better parallelism</li><li class="">improved tilt series alignment (resolution improvement)</li></ul>
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<li class="">General changes:
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<li class="">New browser options for display of stacks of 3-D volumes</li><li class="">RCTboxer works properly again</li><li class="">fixed a problem reading A/pix from FEI-style MRC files.</li><li class="">New Processor for bit-compression of image files (makes images more compressible)</li></ul>
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<p class=""><u class="">SPHIRE 1.3 major changes</u></p>
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>• Support for processing helical specimens (beta).<br class="">
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>• Hands free processing with AutoSPHIRE: While the individual steps can be configured and executed by hand, SPHIRE 1.3 includes AutoSPHIRE, an integrated tool that enables SPHIRE to
run without the need for user supervision up until the creation of a high resolution reconstruction.<br class="">
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>• Per particle CTF refinement with error estimation. When you reach a resolution of about 4Å you can refine your CTF on a per-particle basis. This can improve the resolution by 0.3Å
or more.<br class="">
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>• Integration of crYOLO 1.5 for particle picking. crYOLO is based on convolutional neural networks and can accurately pick about ten micrographs per second.<br class="">
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>• Integration of automatic 2D class selection with Cinderella. This tool is based on a deep learning network to separate 2D classes from .hdf / .mrcs files into good and bad classes.
It uses the same deep neural network as crYOLO and comes pre-trained on a set of good and bad classes. Cinderella was written to automate cryo-EM data processing.<br class="">
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>• The new compare re-projections tool can now be used to produce side-by-side comparisons of the 2D class averages with the respective projections of a 3D model.<br class="">
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>• Visualization of 2D power spectra in CTER.</div>
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<font face="Courier" class=""><span style="font-size: 14px;" class="">--------------------------------------------------------------------------------------<br class="">
Steven Ludtke, Ph.D. <<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a>> Baylor College of Medicine <br class="">
Charles C. Bell Jr., Professor of Structural Biology<br class="">
Dept. of Biochemistry and Molecular Biology (<a href="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a>)<br class="">
Academic Director, CryoEM Core (<a href="http://cryoem.bcm.edu" class="">cryoem.bcm.edu</a>)<br class="">
Co-Director CIBR Center (<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a>)<br class="">
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