[3dem] relion-1.4 release

Sjors Scheres scheres at mrc-lmb.cam.ac.uk
Wed Sep 2 01:52:29 PDT 2015


Dear colleagues,

Please be informed that relion-1.4 is now available for download. It's 
main new features are:

1. SUB-TOMOGRAM AVERAGING
As published in our latest Structure paper 
(http://dx.doi.org/10.1016/j.str.2015.06.026). Detailed instructions are 
avaliable on the Wiki. Apart from the concept (and calculation) of a 3D 
CTF-model, for which Tanmay Bharat wrote some scripts, most things are 
similar to single-particle processing. So, if you hadn't used relion for 
single-particle processing and wish to perform sub-tomogram averaging, 
please do browse through the Wiki pages, and perhaps follow the tutorial 
first.

2. FOCUSED CLASSIFICATION WITH SIGNAL SUBTRACTION
Technically not a new feature, because the main functionality was 
already present in relion-1.3 (though user-friendliness has been 
improved). This new tool is probably our most powerful classification 
approach yet. We demonstrate its results on our gamma-secretase dataset 
that gave a 3.4A map, in which we now find three sub-states. The 
corresponding paper has only just been submitted for publication, but to 
facilitate early uptake of the method we have put a preprint on bioRxiv 
(http://dx.doi.org/10.1101/025890). Detailed instructions on how to use 
this method may be found in the preprint.

3. SPEED-UP
a) Re-implementation of multi-threaded code. Now, many-threaded jobs 
(e.g. --j > 6) scale better than before.
b) Movie-processing is now >10x faster than before.
c) By default, relion_refine_mpi will now read images from ALL 
MPI-slaves in parallel. This was only done by the MPI-master in 
relion-1.3. This will speed-up significantly on parallel file systems 
(we use /fhgfs). However, be careful with large NFS-based system, which 
may not be able to cope with the parallel load. You can go back to 
master-only reading using the --no_parallel_disc_io flag.

4. MEMORY USAGE
There is now an option (in the INSTALL.sh script) to compile the entire 
package in single-precision (the default remains double-precision). 
Reproducibility of these runs is gone, but it saves you 50% RAM. Our 
results indicate that performance does not suffer significantly, but 
admittedly not as many tests were performed with single-precision mode 
as with the other new features. Therefore, your feedback on this feature 
will be much appreciated.

For those of you who participated in beta-testing: thank you for your 
help in making the code more stable! Please update your 
beta-installation to the stable release.

Have fun,
Sjors

-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres



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