Frealign

I am trying multi-reference refinement, but am getting crashes during reconstruction, apparently because the two reconstructions running simultaneously demand more memory than is present. Is there a way to reconstruct the r1 volume and the r2 volume separately, at different times?
Alternately, I guess I could do two runs and specify half of the particles in calc_reconstructions for each, then recombine the two halves for each.

Hi,

In two cases, I need to run frealign without doing CTF correction on the input images: (1) images collected using a phase plate; (2) regular defocused images, but with phase flipped. How can I setup frealign to run such data? Thanks.

Bests,
Xing

Hi,

I would like to generate an output reconstruction and 2 half sets which are NOT masked in any way, but i'm not sure there is a way to do this? When I try and set RO and RI to =0, these parameters are not accepted.

I am using helical mode in frealign v8.09, any help would be greatly appreciated,

Cheers,
Joe

On the software download page for frealign ( http://grigoriefflab.janelia.org/frealign ) a script to convert particle alignment parameters from Relion to Frealign is mentioned, and there is a link. Unfortunately the link just returns a "Page not found" page. Does this script exist? I would like to use it.

Hi，Niko, I am new in using frealign,so I have confused by its output. When running frealign, it appeared that "Best score for particle 1 at Rmin/Rmax 200.0 10.0:*** POWELL MIN： MAXIMUM CHANGE DOES NOT ALTER FUNCTION ". I am wondering what does this mean about "POWELL MIN： MAXIMUM CHANGE DOES NOT ALTER FUNCTION"? Why for some particles it appears several times some never? Thanks!

Lingyun

Dear All,

It seems that I ran into some very silly problem.

I downloaded "frealign_v9.08_140514.tar.gz" on my new MacPro and set it to /usr/local. Following the instruction for installation, I launched the command: tar -xzvf frealign_v9.08_140514.tar.gz which, created the folder frealign_v9.08. Going into the folder (cd frealign_v9.08) , I see the contents - README.txt bin src.

## When I type INSTALL - general install usage options are flashed. I fail to get the line to be put in the PATH variable.

In any case, I put the path in my bashrc file as

#Frealign

Hi,Niko,I am graduate student in Tsinghua University, I am trying to use the latest version FREALIGN released on June 13th, 2014 to do helical reconstruction.But I have encountered a fatal error. When I use give the input parameters needed for frealign, it exits automatically only with a Warning: ieee_inexact is signaling. This warning appeared when I gave the image stack. But with the example for TMV, it ran successfully. So I am wondering is there anything wrong with my image stack file or something else?

I'm having a problem with refinement, and was hoping someone could help.

I have a helical structure refined to ~7.5Å (gold standard approach) using SPIDER, and I wanted to see if using frealign would improve the structure. I wasn't certain that I had converted the angle assignments correctly, so I ran an initial search (mode 4) using a high resolution cutoff of 10 Å. The structure after this first round had a reasonable enough looking FSC curve (see attached, black curve), and a resolution of ~7A at the 0.143 cutoff, and the map looked very similar to the map refined in SPIDER.

Dear Niko,

I have reconstructed two maps from two subsets of data using Frealign v9.08. Then calculated the FSC directly from those two maps (reconstruction.mrc) without any masking. The FSC curve (attached) does not fall down to zero completely at high resolutions but goes up very fast. My mparameters file is as follows:

working_directory /raid2/donghua/DE-20/gset1
data_input DE-20
raw_images1 DE-20_odd_new_stack
thresh_reconst 0.95
thresh_refine 0.9
pixel_size 1.07
dstep 6.4

Dear Niko,

I did reconstruction successfully before with 9.07 version (FSTAT=F, IMEM=2, INTERP=0). After I changed to v9.08 and only turned on FDUMP (=T), the map created was invalid in MRC format and not readable. The log file did say normal termination. I did not feel any obvious speedup, maybe just saved some time because of not creating a couple of intermediate files.

Thanks in advance!
Donghua