Frealign

Hi,

I started to use frealign just few weeks ago and play around with several parameters to improve the resolution.
By chance I realised that the FSC is somehow correlated to the number of cpus used for reconstruction.
The more cpus I use, i.e. the more partial stacks are created, the lower (means worse) the resolution gets.
Is that by any means intended? How many cpus do you usually use for your reconstructions?

Besides that, what other parameters do you consider for obtaining better resolutions?

Best,
tarek

Hi,

I have observed very different results between two different approaches for CTF correction of map reconstructions performed with FREALIGN v9.11 for one dataset that I'm working on:

1st approach: normal CTF correction inside FREALIGN. Defocus and astigmatism values specified in .par file, WGH = 0.07.

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.

Hi Niko,

I have a medium resolution structure of a virus particle which I got using EMAN2 (e2refine_easy). I tried to do a refinement using FreAlign in EMAN2. Unfortunately, the "refined" structure looks less detailed than the input (snapshot attached - input on the left, OutputMap on the right). I am most likely using it wrong/inputting some wrong parameters - where could I be going wrong? Can you please give me some suggestions on how to improve the FreAlign refinement results?

- Convert to FreAlign

Hi Niko, hi everybody!

I read that frealign supports multiple datasets from different collections. How do I use this feature? My datasets have small differences in respect to pix_size and some fluctuation regarding the Voltage between the collections.
I tried simply providing two stacks and .par-files and giving two "# Dataset-specific parameters"-blocks in the mparameters file. When I do this i get: "if: Expression Syntax."

Thanks for the help!

Lukas

Hi all,

We had a symptom that was debugged, which might be informative for the forum.

The "new" Frealign scripts were failing for me, and I was not able to get any output from a reconstruction. Examples of some of the symptoms/errors in 'stderr' were:

line 3: limit: command not found
line 24: syntax error near unexpected token `set'
...
line 128: syntax error: unexpected end of file

Hi,

I wonder how to tell frealign to use a sphere mask with coordinates read out of IMOD's XYZ module. I cannot find the command 'focus_mask' in the mparameters file. And how do I provide the IMOD coordinates that frealign can read them? I just find the settings for providing an external mask by adding the file name in mparameters.

Best regards,
Alex

Hello Niko and others,

I'm preparing the par file and sub-stack image file from relion to run 3D classification in Frealign. Now I have successfully convert

Dear all,

I am trying to submit a job to PBS cluster in working directory, but I don't know how to write a right script.
I tried the following script and with a output file with message "No PBS system available. Submit jobs to local machine (y/N)?"
What should I do to chang my job script?

Best regards!
Jianhao

Job Script:
#!/bin/bash
#PBS -q QUEUE
#PBS -l nodes=3:ppn=12
#PBS -j oe
#PBS -N frealign
#PBS -V
cd $PBS_O_WORKDIR
mpiexec -np 120 --bynode frealign_run_refine

Output File:
21:54:19 up 17 days, 10:31, 0 users, load average: 0.21, 0.20, 0.13

Hello,

Is there a way (or program) to plot the orientation distribution of particles from a frealign parameter file (*.par) so we can visually see the orientation distribution?

Thanks