Mode 0 - reconstruction only

Submitted by Matthieu on Tue, 2016-03-08 16:44

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Frealign

Hi,

I'm new to frealign. In order to get only a 3D reconstruction I tried to use the "MODE 0" (for instance
in the helical_refinement example for v9.11) with the command frealign_run_refine, which gave an error:

$ frealign_run_refine
ERROR: MODE must be 1, 2, 3 or 4.
Terminating...

The mparameter script comment on the MODE line indeed says "1, 2, 3 or 4. Refinement mode, normally 1. Set to 2 for additional search."

Looking in the bin directory for other scripts and running

$ frealign_calc_reconstructions 1

does generate a reconstruction for both MODE 0 and 1.
I've not seen more details on MODE 0 in the README.txt file for v9.11.

So my questions : Is the previous command what I should use to get only a 3D reconstruction without refinement? How can "MODE 0" be used in v9.11?

Thanks,

Matthieu

niko Tue, 2016-03-08 16:52

The README.txt file refers to the frealign_v9.11.exe file which users can run without the scripts if they like. If you use the higher-level scripts (recommended) you do not need to set the mode to calculate a reconstruction - just use the frealign_calc_reconstructions command as you have done. For normal refinement, set MODE to 1. For a global search (slow), set MODE to 3.