Frealign

I built GeFREALIGN 8.06-20110514 from the tarball on this website with the CUDA 4.2 toolkit on a 64-bit CentOS 5.8 machine without any problems. The two binaries compiled and linked without issue. Unfortunately the refinement binary is crashing when I run it. Here's a snippet of the logfile:


Fourier-transform reference volume....
3D WEIGHTS FILE FOR OUTPUT?
3D RECONSTRUCTION HALFSET 1 FOR OUTPUT ?
3D RECONSTRUCTION HALFSET 2 FOR OUTPUT ?
3D PHASE RESIDUAL FILE FOR OUTPUT ?
3D POINT SPREAD FUNCTION FOR OUTPUT ?


I'd like to generate a plot of the euler angle distribution for my asymmetric FREALIGN-refined reconstruction. What are the most common ways of doing so in FREALIGN given that FREALIGN has refined the original euler angles?

Do people write scripts that go through and find all neighboring euler angles to group them together? If so, how do you go about doing this?

Many thanks,
Mike

Hi,

Dear all,

I try to convert my spider alignment file to Frealign parameter file. It always results a sphere in the reconstruction. I suppose something is wrong with my angles, but I couldn't figure out what. Here is the corresponding part of the script I'm using (input for the angles is the doc file from 'ap ref' in spider):

PSI=`cat alignment_1_00001.spi | awk NR==$a | awk '{print $8}'`
THETA=`cat alignment_1_00001.spi | awk NR==$a | awk '{print $4}'`
PHI=`cat alignment_1_00001.spi | awk NR==$a | awk '{print $5}'`

Dear all,

I would like to use frealign_v08.09 and after I prepared the image stack file containing the particles and the EM map, when I send the script I get the following error:

#PGFIO-F-217/list-directed read/internal file/attempt to read past end of file.
 In source file card6.f, at line number 27
0.000u 0.001s 0:00.01 0.0%      0+0k 8+8io 0pf+0w
cp Frhnegtilt_params_1.par /home/luciccar/Frh-tilt-pairs/ccd/test2/.
cp: cannot stat `Frhnegtilt_params_1.par': No such file or directory

In BPV case, FBEAUT and FCREF are set to F (at final cycle). Do we need to use them at early cycle? Why turn them off in final cycle? Is it anything to do with Ewald correction or B (-80.0) factor?

The BPV data set apply beamtilt correction (-0.01, -0.01). How do you get these numbers?

Many datasets set defocus uncertainty to 50.0. Do we need to worry about it? Or just leave it untouch?

The parameter, phase residue target: according to README, we should set it small, like 15.0. But I check couple data sets in your website, DLP and TMV are set to 82.0, 7RP set to 60.0, and BPV set to 30.0. I wonder what is rule to adjust this parameter? I found those datasets, DLP or 7rp with target residue at 82., their phase residues in par file are around 60 to 70 and dataset BPV with target residue 30, their phase residues are around 80 to 90. I am confused.

Dear Niko,

I run Frealign_v8_mp.exe very well for the 3D reconstruction with several cores on a single computer. The reconstruction job is divided onto multiple cores of my computer.
Now I would like to run Frealign reconstruction on a cluster using multiple nodes. Is there any script to do so? I searched your forum but did not find any.

Thanks in advance!
Donghua