Unblur & Summovie

I would like to sum frames 2-10 out of a stack of 40. First I used Unblur to align all 40 frames and generate a shifts.txt file. Then I used Sum_movie to sum frames 2-10. My question is, after I specify starting frame as #2 and the dose rate, what should I put as the pre-exposure: 2.2 e/A2 which accounts for the 1st frame, or 0 if the program already knows we start from frame 2?

We were wondering whether the algorithm is robust to the initial few frames being included (especially if there are charging or other big differences in the first few frames). Is it good standard practice to exclude the initial frames of the movie when processing with unblur? Does the algorithm use the middle frames as the reference?

Hello,

I want to compile unblur on ubuntu 14.04 64bit. First of all configure throws warnings "rm: cannot remove 'core': Is a directory":


# ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/usr/local/src/unblur_1.0.2/src/missing: line 1: syntax error near unexpected token `<<<'
/usr/local/src/unblur_1.0.2/src/missing: line 1: `<<<<<<< .mine'
configure: WARNING: `missing' script is too old or missing
checking for a thread-safe mkdir -p... /bin/mkdir -p


Hi all,

I am now using Unblur and Summovie to process my data. I am curious to know what the Guinier plot usually look like with the dose filter applied and noise power restored, is the b-factor going to be smaller than reconstruction without the filter? Or is a linear fit of b-factor agrees well with the experimental map amplitudes decay?
Thanks a lot.

TAT

Dear all,

Recently I tried to compile unblur in my mac (OSX 10.9) using gfortran instead of ifort.

I used the following command

./configure FC=gfortran F77=gfortran LDFLAGS=-L/usr/local/Cellar/jbigkit/2.1/lib/ --enable-openmp --prefix=/pathtomyinstall

Hi Tim et al,

I've been trying to use unblur on individual particles with a box size of 128x128 px. It appears to be performing poorly, the aligned particles look worse than a sum of the original unaligned particle stack. Is there a lower limit on the micrograph size for unblur to operate well?

Attached are sums of the original unaligned stack and the aligned stack for a particle.

Cheers,
Matt I

Hello,

we are currently trying the unblur dose filtering on a 20S test dataset, acquired on a Falcon 3 with a total dose of approx. 70 e A^-2 over 2 minutes.
The frames have been aligned with another program and I used the aligned frames with a dose of 2 e A^-2 per frame for the dose filtering procedure using summovie and handing over shift files with zeros in all shift entries.

To evaluate the dose filtering I compared the refinements done in RELION of the following three datasets:
a) particles extracted from aligned sums

Hi Tim,

When doing ctf estimation, should I use motion-corrected and dose-filtered sum or simply the motion-corrected sum?
I have used the former. Because I thought particles from these sums are used for all further processing.
Could you please explain what's difference and which one I should use?

For comparison I tested 10 micrographs using ctffind4 and the results are pasted below.

Thanks,
Wei

motion-corrected and dose-filtered sum:
21861.669922 21284.919922 45.610001
23154.029297 22563.410156 29.959999
24590.570312 23808.759766 29.600000

Hello everyone,

using summovie with frame weightening with my frame data I seem to see the mask for weightening very strongly in the powerspectra. In other testdatasets from the empiar database I don't see this problem and I am wondering where this might originate from and wether this will be a problem in my further image processing as it appears to be rather sharp edges. I attached to exemplary powerspectra.

thanks kind regards

David

Dear all,

I'd like to try the unblur program, but some of my frames were collected as a sum of two or more individual frames.
"""
frames 1-5 are 1 frame
frame 6 is sum of 3
frame 7 is sum of 4 frames
"""
Is there a way of specifying a different dose for each frame in the movie?

Thanks,
Martin Turk