Single Particle Reconstruction

The reconstruction can then be done from the selected particles. Typically, two maps from different halves of the selected particles need to be generated to determine resolution. These two maps can be added afterwards to give the full map. The program breconstruct has several options to do the reconstruction in different ways, depending on the desired outcome as well as the capabilities of the computer being used. Here are a few cases:

1. Reconstruction options

1.1 A simple reconstruction:

The main decision is to what resolution the reconstruction should be calculated:

breconstruct -v 3 -resol 15 -rescale 0,1 -sym D5 -CTF baseflip -recon klh_run1.pif >& klh_run1_rec.log &

1.2 Two half set reconstructions and a full set reconstruction:

All three maps can be calculated at the same time:

breconstruct -v 3 -resol 15 -full -half -rescale 0,1 -sym D5 -CTF baseflip -recon klh_run1.pif >& klh_run1_rec.log &

The resultant maps from the half sets have the inserts "_01" and "_02" before the extension. These maps can be added to generate a single reconstruction that is the same as the full set map:

bop -v 7 -add 1,0 klh_run1_01.pif klh_run1_02.pif klh_run1.pif

1.3 Threaded reconstruction:

If Bsoft was compiled with Grand Central Dispatch (Mac OSX) or OpenMP and FFTW3 support, the reconstruction can be run with multiple threads:

breconstruct -v 3 -resol 15 -full -half -threads 8 -rescale 0,1 -sym D5 -CTF baseflip -recon klh_run1.pif >& klh_run1_rec.log &

Be aware that this is very memory-intensive, requiring 20 times the map volume per thread. For example, a map of size 500^3 will require about 2.5 Gb per thread.

1.4 Selected reconstructions:

Reconstructions can also be done from specific selection numbers in the parameter file using the "-classes" option:

breconstruct -v 3 -resol 15 -full -half -classes 1,3-5 -threads 2 -rescale 0,1 -sym D5 -CTF baseflip -recon klh_run1.pif >& klh_run1_rec.log &

In this case the threads are per class, and for calculating halfmaps in each class, the number of threads should be even. Because of memory limitations, it is likely better to specify only one class per run.

2. Resolution determination

The two reconstructions are then compared to determine the resolution:

bresolve -v 7 -resol 15 -Post -map klh_run1_01.pif klh_run1_02.pif

The resolution curves for FSC (Fourier shell correlation) and DPR (differential phase residual) are written into the postscript file in such a way that it can be opened in a graphing program that can interpret text files (Kaleidagraph or Excel).