Frealign

Hey everybody,

I am by no means a programmer, and I have limited experience working on a cluster, but I was wondering if anyone has tried to modify the submission scripts in mult_refine.com to submit the multiple refinement jobs as an array to free up nodes on the cluster.

I was thinking something along these lines might work (The lines I inserted are comments right now, also I run on a PBS cluster):

if ( $sym == "H" || $sym == "HP" ) then
echo ${bin_dir}/mult_hrefine_n.com $fst $lastn $start $nc 1 0 0 0 0 0 >> $SCRATCH/pbs_${fst}_${nc}.com


Hi everybody,

Hi,

Do you have an example to demonstrate how to read in a set of symmetry matrices for an undefined symmetry group? Should I provide the matrices in the "mparameter" file? Thanks.

Xing

I am wondering the largest the image size that frealign can handel. I have something that might exceed 1024*1024, is it possible.

I am running frealign 9.09 on a MOAB/TORQUE cluster. frealign_run_refine is working well for me. However, there is a feature that is either not working or that I'm using incorrectly. My understanding is that In the mparameters file, the nprocessor_rec parameter is the number of independent reconstructions to perform and mp_cpus is the number of threads to use in each of the reconstruction jobs. However, when I run a job with mp_cpus >1, the submitted job only ever uses 1 processor. Am I mistaken about how to set up the mparameter file, or is there something else going on here?

Thanks,

I am switching from 8.11 to 9.09. The refinement seems went well but the reconstruction does not generate valid output. In the end, the log shows
"Time before particle 1 was 14:42:14
Time before particle 2 was 14:42:14
Time before particle 11 was 14:42:16
Time before particle 100 was 14:42:35

PARTICLES BELOW THRESHOLD (NOT INCLUDED) IN SET 1: 45
55 PARTICLES FOR OVERALL SCORE CALCULATION
SCORE (between resolution limits) = 7.625455
AVERAGE OCCUPANCY = 100.000000

Hello,

We are attempting to run Frealign Maximum Likelihood classification on our cluster, and have run into some issues. We can run Frealign using a single reference without any issues, or multi-class runs run locally, but multi-class runs on the cluster will crash in the initial cycle. Here is the final lines of a log file:

Cycle 0: reconstructing particles 1 to 15684 on Wed Nov 19 13:55:05 EST 2014
Cycle 0: reconstruction for particles 1 to 15684, ref 1, finished Wed Nov 19 14:10:16 EST 2014

Hi, in the README file, it says " Weighted correlation coefficient now uses SSNR table from the previous iteration for more accuracy."
How exactly does frealign get this SSNR table? Should I include the FSC table from last iteration to my .par file ?
If I don't specify the SSNR table, will frealign simply use a linear scoring function?

Thanks!

Rui

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

Hi there,

I am using the latest version of Frealign 9.09 (I also got this with 9.08) and I am having a extrange behavior during my 3D refinement. I used data binned by 2 (pixel size 2.0A/px) and obtained a structure that I would like to keep refining with my unbinned data. I copied the last .par file from my refinement and I updated the magnification column and used that as the initial parameters for new cycles of refinement with my unbinned data.