question about FDUMP

Submitted by Rui Zhang on Sat, 2014-11-15 12:51

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Frealign

Hi,
This is the first time I try frealign version 9 (v9.09).
I find if I set FDUMP to T, frealign doesn't output odd/even maps, and no FSC table in the .res file. And I don't see a merge_3d_r${1}.in file.
However, if I set FDUMP to F, I can get odd and even maps and FSC table.
Is it something expected?

Thanks!

The flags I use are:

time ${bin_dir}/frealign_v9_mp.exe << eot >& ${data_input}_mult_reconstruct_r${4}_n${1}.log
M,0,F,F,F,F,0,F,T,F,F,0,F,0,1 !CFORM,IFLAG,FMAG,FDEF,FASTIG,FPART,IEWALD,FBEAUT,FFILT,FBFACT,FMATCH,IFSC,FDUMP,IMEM,INTERP

niko Sat, 2014-11-15 18:05

Yes, FDUMP=T will dump all intermediate files into one output file. The dump files from different Frealign runs can be read by merge_3d and merged into a single 3D map with all the output files that are normally generated. Please use the scripts that come with the latest distribution to make use of this new feature, which enables fast parallelization of 3D reconstruction.

Rui Zhang Sat, 2014-11-15 19:02

Thanks for the explanation!
However, I don't see a merge_3d_r${1}.in file that I can run the script, although the log file says "Normal termination of frealign".
I am running a single-reference refinement.
Any ideas?

niko Sat, 2014-11-15 20:02

Please run the included scripts to make use of this new feature. Otherwise, please ignore the feature. Please also consult the online help pages for further info on how to run the new scripts.

Rui Zhang Sun, 2014-11-16 20:30

After manually run ~/bin/frealign_v9.09/bin/merge_3d_mp.exe, I realized the only output file named data_r_n1.mrc is actually a dump file instead of a regular 3D map. Thanks!!

P.S. I think a previous post probably had the same confusion as I had since he mentioned "the map created was invalid in MRC format and not readable".
http://grigoriefflab.janelia.org/node/4468