Frealign

Dear Niko,

I have one question about card 7. In my log file attached at the end, there is one line:
RESOLUTION RECONST., REFINE LOW/HIGH, CLASSIFY, DFSTD, RBFACT ?
And the input was shown as
3.0 200.0 3.4 3.4 100.0 150.0

Does this mean RBFACT=150.0? or RBFACT not shown in the log file?
Is DFSTD ( DFSIG ? ) defaulted to be 100.0?
In fact RBFACT was set to zero and DFSIG was 150.0 in my mparameters file.

Thanks!
Donghua

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FREALIGN - Fourier REconstruction and ALIGNment
V9.08 - 05.05.14

Hi,

In Matthias Wolf's 2010 papillomavirus PNAS paper, you mentioned
"All contrast-transfer-function para- meters were recalculated using the improved pixel size followed by an additional three cycles of refinement and reconstruction."

I wonder did this step significantly improve the resolution?

Thanks!

Rui

Hello,

I have I have been using the older version of Frealign (v7.07) in the past and am starting to switch to the latest version (v 9.07). With that, I have a few questions regarding to the parameter files in the newer version:

1) In the output parameter file, phase residuals have been replaced with a score to indicate the quality of fitting where a high number indicates good fit. What is the range of these scores?

2) In the output parameter file, what do the numbers for OCC, -LogP and Sigma mean?

Hello-

I'm wondering if support for MRC format stacks / volumes has been removed from FREALIGN v 9.06 and 9.07?

I'm getting the following error with both:

Warning: ieee_inexact is signaling
ERROR: DATA FORMAT NOT SUPPORTED
PARTICLE IMAGE STACK ?
/spin1/users/alushing/fact_vinc/7and14mar_combined/frealign/REF1/stack.mrc

Opening SPIDER file for READ...
File : /spin1/users/alushing/fact_vinc/7and14mar_combined/frealign/REF1/stack.mrc

Hi Niko:

Trying run your new tests (the test that is in search directory) with both new versions frealign_v9.06 and frealign_v9.07, I had the following error:

PGFIO-F-235/formatted write/unit=6/edit descriptor does not match item type.
File name = stdout formatted, sequential access record = 51
In source file card10.f, at line number 373
0.000u 0.002s 0:00.00 0.0% 0+0k 0+0io 0pf+0w

The commands that I ran were:

cp -p pdh_1.mrc pdh_2.mrc

time ../../frealign_v9.07/bin/frealign_v9.exe << eot

The latest frealign
Maximum likelihood multi-reference classification (no helical processing),
I wish to have a set of demo scripts

Thanks
XM

Hi,

I collected two datasets of the same sample, and I first did reconstructions from the dataset #1. But when I used the final reconstruction from the dataset #1 as the model for the dataset #2, I found that the reconstruction from the #2 dataset has a flipped (wrong) handness! Is there any way to flip back the handness during refinement with frealign? Set "FLIP=T" in mparameters? Thanks much.

Xing

Hi,

i was hoping to generate some variance maps, I guess via the bootstrap resampling technique. I see this is possible in eman2 and sparx but I was wondering what the best way to do this is when I have already performed a refinement in frealign, therefore I have a frealign parameter file for all particles, and an image stack in spider format. I am running frealign version 8.09. Any help would be greatly appreciated!

Cheers,
Joe

Hi Niko,

Hi, can anyone explain what the option FFILT does in FREALIGN?
To me it works as a low-pass filter but I am not sure.

Thanks!