Frealign

Hi,

I calculated a variance map from 1000 bootstrap volumes, my dataset was downsampled by a factor of 2 with resample_mp.exe, and the resolution of the reconstructed bootstrap volumes was limited to 8 A. And I imposed C4 symmetry. FBEAUT was set to F.

In the resulting variance map I get a strong "column" spanning all slices in the very middle of the box, parallel to the Z-axis. I understand this as a symmetrization artifact (no symmetrization is imposed on the central voxel column?), but not sure. The rest of the variance map seems to make sense.

Top view: http://imgur.com/B2AuHX7

Dear all,
I am processing a particular data set that due to sub-optimal imaging
conditions has beam tilt (probably has also difference in magnification between images/particles
and perhaps other pathologies). If I want to do a grid scan for the beam tilt in X an Y, should I just type the values in mparameters
file (example 1,1 and 1,2 etc.,) and look for the values that gives the best reconstruction ?

I tried doing this by typing in the values but in the output parameter value the beam tilt values are still default at 0, 0.

Hi,

I am getting a segmentation fault error originating in function AINTERPO3DS (v9.11 151031). Backtracing gives:

Final lines:

frealign_v9.exe 0000000001ABC9DF Unknown Unknown Unknown
frealign_v9.exe 0000000001AC03FD Unknown Unknown Unknown
frealign_v9.exe 0000000001B731C0 Unknown Unknown Unknown
frealign_v9.exe 0000000000451A76 ainterpo3ds_ 88 ainterpo3ds.f
frealign_v9.exe 00000000004461F9 presb_ 104 presb.f

Dear all,

I'm very new to Frealign. I get Frealign running. The result looks wonderful. However, there are a lot of questions to be asked:
1. If I understand correctly, Frealign FSC is not Gold Standard FSC. How to prevent overfitting apart from setting the refinement high resolution cut off lower than the current res estimated by FSC? Even if we don't have overfitting issue, what should we say if ever publishing the data (it is not gold standard FSC)?

Hi Niko,

I recently tried to use frealign to determine my particles' initial orientations, and I could be able to start the job normally after typing frealign_run_refine and no error info coming out in the frealign.log file, but somehow the job can not go forward and I got an error message “ls: no match” when the command mult_refine_n.com was executed. Do you have any idea what could cause that problem?

Any advice will be highly appreciated.

Best,
Zhihai

Hi,

I've been using frealign for a while now with awesome results (helical refinement for microtubule structure), but recently I collected a dataset on a new setup (krios + k2) and for some reason my FSC curve is looking very strange.

The FSC curve from my initial backprojection looks just fine, but after a round of frealign refinement followed by backprojection (14pf_r1), I get this weird feature where the FSC starts to increase again at high spatial frequencies ( < 2.6 Angstrom)
Also troubling is that the FSC curve from the refined alignment parameters does not drop to 0.

I found a general general description for doing a virus asymmetric reconstruction with frealign here:http://grigoriefflab.janelia.org/node/2014.

Does anyone have any information on how to use the asymmetry scripts mentioned on that link to do a phage reconstruction? I've already completed the symmetric reconstruction with Frealign and I have an initial model from Auto3DEM.

Hi everyone,

Not sure if this is news to many of you, but I thought I'd share this here in case anyone has experienced similar problems, and to avoid that others get stuck with the same issue:

Hi, Niko ,
I sole the mkl problem , but get a new error message. It looks like is involve with fftw .
I just have fftw-3.3.6 installed , Do you have any idea what cause this error?

gfortran merge_3d.o frealign_v9.a -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ../bin/merge_3d.exe
frealign_v9.a(fftw_plans.o): In function `fftw_plans_2d_':
fftw_plans.f:(.text+0x28): undefined reference to `fftwf_plan_dft_r2c_2d'
fftw_plans.f:(.text+0x42): undefined reference to `fftwf_plan_dft_c2r_2d'
frealign_v9.a(fftw_plans.o): In function `fftw_plans_3d_':

Hi, Niko ,
I have get several error in compile frealign in my linux computer.
According to the log , it need mkl installed . is it right ? do I must install it? Seems not free to get it.
Thank,
Zhao

Here is my log :

sudo make -f Makefile_linux
[sudo] password for zhaow:
gfortran -O3 -s -fomit-frame-pointer -Wall -falign-functions=4 -funroll-loops -fexpensive-optimizations -fschedule-insns2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -cpp -w -c fftw3.3.f90