Frealign

Hi,

During a recent project, I plotted the particles' euler angles before and after a few rounds of mode 4, DANG 20, ITMAX 200 (frealign_v9.11). Attached you can see that a small portion of the particles now line up along the meridian of each of the graphs. More rounds of mode 4 or refining through mode 2 and 1 do not remove this feature. Could this be from some preferred orientation of the particle in ice or am I assaying too many orientations with mode 4 at such a fine angular step? Has anybody seen this before?

We have a ribosomal data set that goes down to ~3Å resolution, with which we’ve been conducting numerous tests. The data was collected in super-resolution mode, and an unbinned stack (pixel size 0.6565) was assembled. Additionally, the stack was Fourier binned by 2 using resample_mp.exe to a pixel size 1.315 and refined in an identical manner. Both stacks were normalized to mean 0 and std 1.

Hi, I am trying to run Frealign v9.10 but got Segmentation fault
Segmentation fault (core dumped)
1.606u 26.363s 0:28.65 97.5% 0+0k 52288+56io 2pf+0w

the exact script will run if I specify Frealign v9.09 instead

Comparison of the log files shows the program stops right before "3D MAP FILE FOR INPUT?"

Thank you!

C Date and time 17-08-2015, 17:12 Frealign V9.10 - 18.05.15
C Image format . . . . . . . . . . . . M
C Mode . . . . . . . . . . . . . . . . 1
C PMASK for parameter refinement . . . 1 1 1 1 1
C Magnification refinement . . . . . . F

Just as an FYI bug report, I had a job crash with a negative magnification during mag refinement. I attached the relevant log. Note there are a bunch of null chars in the .log in the Titles. This appears to be something that happens when importing a particle stack from Relion using relion_stack_create.

The job is now running without mag refinement.

Hi Niko,

Is there any way to apply the parameters in the .par file (I am using an old version 8) to the frealign image stack (spider in this case) to create an output aligned image stack?
If I can not do this directly inside frealign, I suppose I would have to convert the par file.. any suggestions?

This is so that I can do 2D classification (would have to be outside of Frealign) to remove junk particles.

Cheers,
Joe

Hi,

I have been running frealign_run_search (MODE 3) on a relatively large data set for six days on our cluster. While I am happy so far with the results according to the reprojections (FMATCH = T), I don't know how long it will take to complete the job (days? weeks? months?). Therefore, I have the following questions:

1) Is it possible to somehow estimate the total running time?
(e.g. accounting for the # of images, image size, target resolution, CPUs, etc)

2) What are the recommended procedures for tracking the intermediate results?

Thanks,

Ricardo Righetto

Hi everybody,

Our HPC at FSU just migrated to the SLURM resource manager instead of PBS that they were using previously. Unfortunately, now the frealign_run_refine script doesn't work for us. The computer section of my mparameters file looks like this:
# Computer-specific setting
cluster_type SLURM ! Set to "sge", "lsf", "slurm", "pbs" or "condor" when running on an SGE, LSF, SLURM, PBS or CONDOR cl
uster, otherwise set to "none".
nprocessor_ref 4 ! Number of CPUs to use during refinement.
nprocessor_rec 4 ! Number of CPUs to use during reconstruction.

Dear Frealign developers,
I am told that Frealign has the mask option and I want to try it out.
I have just downloaded the latest version V9.10. But when I type frealign_template, I didn't find those masking settings.
I am wondering if I downloaded the wrong file or the template with mask option is not public available yet?
Thanks,
Lei

/t1/lei/soft/frealign_v9.10/bin/frealign_template

# Computer-specific setting
cluster_type none ! Set to "sge", "lsf", "slurm", "pbs" or "condor" when running on an SGE, LSF, SLURM, PBS or CONDOR cluster, otherwise set to "none".

I noticed there is now a mode 5 listed in the mparameters file in Frealign 9.10 as well as some other small changes; however I did not see any mention of mode 5 in the README.txt. Looking at card10, it looks about the same as the previous version with no mention of mode 5. Is there a desciption available?