Carsten Sachse
Dear Spring users,
We are happy to announce an version of Spring. Find our latest publication high-resolution application using direct-electron detector TMV data at J Struc Biol 2015 (in press).
Follow update instructions at:
http://www.sachse.embl.de/emspring/install.html#update
1. Installation procedures
* Updated dependencies GCC, Numpy, Scipy, Openmpi including build procedures.
2. SEGMENTREFINE3D
* Computation of persistence length at the end of each refinement run. Can be used now as a selection criterion for discarding less straight helices in the next refinement run.
* Selection criteria: Straight helices, Layer-line correlation and Projection matching cross-correlation are now selected in percent range of the distribution instead of cutoff values, e.g. upper 20 % --> 80 - 100 %.
* 'Continue refinement option' - in case no reference structure is given a 3D reconstruction based on the provided parameters is now created for further refinement.
* Improved segment-based motion correction, now accepts mrcs-stacks.
* Computation of structure-masked FSC with mask deconvolution according to Ultramicroscopy Chen et al. 2013 (Scheres and Henderson) for resolutions better than 12 Angstrom.
* Added error estimates for forward x-shift, forward out-of-plane tilt and in-plane rotation angles according to Sachse et al, 2007 J Mol Biol.
* Overhaul in symmetrization of volumes to make them perfectly even.
* Diagnostic power spectra are now always written out as EMAN2 image files in addition to diagnostic summary.
3. High-performance computing cluster
* Added support for SLURM.
4. SEGMENTCLASS, SEGLAYERLATTICE
* Many minor fixes.
Note: old refinement.dbs and grid.dbs need to be upgraded to be readable by the latest Spring version.
% spring -udb='grid.db' -inp grid.db -out grid_upd.db
% spring -udb=refinement.db -inp=refinement024.db -out=refinement024_up.db