Frealign

I was wondering how the "focus_mask" parameter worked, and whether you had any advice on using this in refinement/classification, and how small a region I should expect to be able to work with.

Thanks a lot!

Axel

Hi,

I would like to refine an entire (unmasked) virus in asymmetric mode. If I switch from icosahedral (I) to asymmetric (i), and do not specify any masks, will the structure change from its initial reference?

I'm unclear how exactly the reconstruction uses symmetry-related orientations to bring out asymmetric features. It seems like all 60 orientations are being used for the reconstruction. Without a mask, are the orientations for a single particle evaluated against each other to determine which orientation has a higher likelihood?

Thanks,
Matt

Hi all,

I generated an initial model for an icosahedral virus following the scheme outlined in the 2016 Frealign paper. It's working great so far, but I have some general questions on strategy. After 16 cycles of MODE 3, and with a 30 A resolution limit, my FSC now extends beyond 10 A. Do you recommend switching to MODE 1, or should I continue to increase the resolution limits while in MODE 3?

Dear all,
I'm running frealign/v8.09 to do the local refinement and 3D reconstruction for MT structure.
The first 4 rounds are pretty fine,but after the 5th round refinement,the map became much worse.
I checked the .par file,it shows that from round4 to round5, the euler angles changed a lot.
But as follow,the mode I'm using is MODE 1.
I'm wondering have you met this kind of problem before,if yes,what can I do the figure this out?

Thanks a lot,
Claire

round5 .par file

C Date and time 30-07-2017, 14:25 Frealign V8.09 - 06.07.10

Hi everyone,

I am a frealign new user. I use Region did 2d classification and use Select in relion2 selected the good particles. Then I use the script on the website converted the star file to par file. But after I run frealign, it still shows the error about parameter file.

Starting refinement...
ERROR: Something wrong with parameter file.
If input file contained film#, defocus 1, defocus 2, astig. angle,
please make sure that numbers are separated by spaces, not commas.

Does anyone have suggestions about it? Thank you very much!!!

Best regards,
Chao

Hello,

I'm using Frealign to generate an initial model of a virus. I saw in an earlier post that it was suggested to set DANG to 0 for MODE 3 initial model generation. When I did this for cycle 1 (with 40A res limit), Frealign set DANG to 8 degrees, which would've taken 40+ hrs, and seemed like overkill for generating a featureless sphere. I set it back to the default 200, but am wondering as I lower the resolution threshold in subsequent cycles if I should also adjust the angular step size.

What do you suggest for DANG at various resolution limits?

Thanks!

Matt

Hello,

We are trying to refine structure with FrealignX, but the Part_fsc value never went down below 0.143 to give a resolution estimation at global search. This has occurred for a few datasets in the lab. We are wondering what the reason could be?

Thank you so much for your time!

Hi specialists,

I found that when I stop frealign with "frealign_kill", some programmes still running if I checked with command "top".
Could I clear all running programmes?

Thanks in advances!

Best regards,
Jianhao

Dear all,
I am new to frealign, so I am following a Methods in Enzymology 2016 paper. I am running in MODE3 and I want to look at matching projections. When I run frealign_calc_projections from a working directory I get:

$frealign_calc_projections

ERROR: particle parameter file not found.
Terminating...

What am I doing wrong?

Thanks!

--
Mike Kopylov,
PhD candidate, Dr. Stroupe group
Institute of Molecular Biophysics, Florida State University

Dear all,

I am trying to squeeze out any fourier pixel possible from a sample dataset and therefore ran the same data with different tools.
I just realized that the resolution achieved by Relion2 is notably better than what I get from frealign.
To avoid any difference in normalization, internal weighting etc. I directly reconstructed the volume using parameters determined by relion with frealign_calc_reconstructions: 4.59A
after 20 iterations of local refinement (mode 1) I end up with 4.92A.

Did anyone experience something similar before?
Any ideas what is going on?

@Niko