Frealign

Hi Everyone!

I am trying to determine the local resolution of my final map using the ResMap tool. This requires the input of two halfvolumes. Can I in principal use the halfvolumes in the scratch folder (3D reconstruction halfset 1 and 2)? What do I need to consider when doing this?

When I inspect these in chimera (e.g. at step 8), i get several parallel density layers spanning the volume of the entire spherical mask. I can only see my particle when I filter very harshly. And even then the map looks very strange (like geographical contour lines).

Hi,

I am refining using frealign version 9.11 151013 and during reconstruction frealign crashes with this error message:

NX, NY, NZ: 256 256 144865
MODE : real
Min, max : -5.532688 5.087115
Mean, RMS : 0.7233188E-02 1.003473
TITLE 1: Relion 1.4 12-Nov-15 11:09:02

Time before particle 9056 was 14:20:28
Cannot seek in file ...
mreconstruct.com finished
Terminating...

Have you seen this error before?

Thanks,
Jon

Dear FREALIGN developers,

Hi everyone!

I am looking for help creating very large stacks for frealign. My current project has 200k particles at 420x420 pixels.

Background:

Hello,

I am having trouble executing multiple jobs in parallele on our SGE cluster.
I am using the below specified mparameters and running frealign_run_refine on the head node. As expected 30 Jobs are queued and start runnning. One exemplary log file (the other 29 are the same):

scratch/test_c5_mult_refine_n_r1.log_1_708:

/bcm/opt/cryo/frealign/frealign_v9.11/bin/frealign_v9.exe: Command not found.


The path is correct, I already checked this.

mparameters:

# Computer-specific setting


Hello-

I am trying out the latest version of Frealign (9.11) on a helical reconstruction of actin filaments in complex with a binding partner. I had previously run a refinement in v9.07.

Hi Niko,

I have been refining my structure using frealign 9.11 12.10.15.

Setting XSTD to 4.5 causes a crash of frealign, when setting it back to 0.0 it runs fine. Is this a problem you have seen at Janelia?

Best,

Axel

Hi everyone,
I converted the post-refinement results from relion and was trying to switch to frealign.
First I use the conversion script to convert relion star file to par file.(http://grigoriefflab.janelia.org/frealign_conversion_scripts)
Then I use relion_stack_create to generate the particle stack.

Frealign could run and finish without error (V9.11).
However, no matter how I changed the parameter, I could only get a feature-less ball.

I am not sure which step went wrong.
Any input will be greatly appreciated.

Below is my mparameters file.

I assume this is a bug, as the reconstruction works fine when 0.0 is used for a single particle reconstruction.

Axel

Hi,

I am wondering what exactly is the role of the mol_mass parameter in the refinement? Is it employed in the definition of the particle Wiener filter [1]? Or is it just used to compute the final map threshold?

Thanks,

Ricardo

References