Unblur & Summovie

Hi Tim,
When I set "apply dose filter" to "yes" in unblur, is the aligned frames also dose-filtered or simply with the shifts applied?
Thanks a lot,
Jing

Hello everybody,

I have been using UNBLUR to align frames from Falcon detector, it works well with 16 frames and 520Mb files. Now I am using K2 detector, and the frames from this detector are not "stack". I am using a Relion script to stack the 32 frames (52 Mb each) and the output is a .mrcs file (1.8 Gb each). I changed the format to mrc and tried to run UNBLUR but there is an error and the images are deleted. Sorry, I am a beginner, could you give some advise?

Thanks

Pablo

** Welcome to UnBlur **
Version - 1.0.2

Tim

I am collecting some data at FSU with the rectangular format (5120 × 3840) DE20 camera.
Can UNBLUR handle this frame size adequately and has anyone used it on DE movies?

I know that DE has its own software for movie frame alignment, but I am used to using
UNBLUR, so if it works...I could evaluate initially with the resolution predictions from
the ctf programs (CTFFIND and GCTF), before proceeding with further processing.

C Akey
Prof

Hi everybody,

I have been trying to use the dose weighting of Summovie to improve my final reconstruction.
Initially I used sums without dosage correction, thereby I reach a final resolution of 3.3A. I then wanted to try the dosage correction.

For this I created new sums of my previously aligned movies. I used the par file of my 3.3A Volume and the particles from the new dose filtered sums, I end up with 4.24A, which improves to 3.95A after another 4 rounds of refinement. My movies consist of 10 frames with a dose of 3.1 e/A²/frame and a pre exposure of 4.6 e/A².

Dear All,

I am running unblur for the stacks.
Is it possible to run it by setting all the input/output/parameters into one single command line instead of typing in the parameters one by one? So that it is easier to run unblur for many stacks.

Thanks so much.

Cheers,
Yingyi

Hi Tim,
I'm considering an unblur wrapper inside relion-2.0. I was thinking of only using your frame alignment method, and leave the dose-weighting up to relion's polishing. Also, I was thinking of avoiding any of the advanced settings. In that case, does the pixel size (in Angstroms) parameter actually do anything else than providing the correct units for the plots? Is there any internal weighting that would be affected by it? If not, I was thinking of setting it always to 1.0, and that way make plots of shifts in pixels.
Thanks for your time,
Sjors

Dear Grigorieff lab,
do you think that I can use the SumMovie for dose filtering on movies collected on DE20 camera? Is it possible to apply the dose filtering with supplied boxes to get back already boxed particles with applied dose filter?

All best,

Gabriel

Dear Unblur experts,

I want to give exposure filtering a try for a ribosomal test data set.
Since I have already pre-aligned particle stacks, I thought I can skip the alignment procedure within unblur and just run summovie with shifts 0,0.
According to your eLife 2015 paper, the filter function was developed for a VP6 sample and also applied to proteasomal particles, which both only consist of proteins.

First of all I'd like to know if you redetermine the filter function for different biological samples.

I have an unblur issue and wondering if there is any way to fix.

I collected some data directly with gatan DM program and saved as mrc stack. when I run the latest version 1.0.2 "unblur_openmp_7_17_15.exe" I got the following message
"2016-02-26 15:33:05: Fatal error (ImageFile::ReadSlicesFromDisk): Array is not properly allocated"

I also check the file by header and here is what I got:
################

[yhl@localhost ~]$header r_cc_0001.mrc

RO image file on unit 1 : r_cc_0001.mrc Size= 1333490 K

This is a byte-swapped file.

Niko

I was wondering, based on a comment in your paper, about whether when using
the unblur, dose corrected ptcls in Relion for refinement, that one could
in fact also polish these particles successfully using the steps in Relion with
the original movies.

It seemed from your paper that you were/are developing your own approach to
the per particle tracking problem.

cheers

C Akey