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mag_distortion_estimate specifications

Information


Unique identifier OMICS_26906
Name mag_distortion_estimate
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A set of images of polycrystalline gold and an estimate of the pixel size.
Input format MRC/CCP4
Output data Some estimated anisotropic magnification parameters.
Operating system Unix/Linux
Programming languages Fortran
License Janelia Farm Research Campus Software Copyright 1.1
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes

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  • person_outline Nikolaus Grigorieff

Publication for mag_distortion_estimate

mag_distortion_estimate citations

 (5)
library_books

Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination

2018
Sci Rep
PMCID: 5799190
PMID: 29403017
DOI: 10.1038/s41598-018-20107-8

[…] ve the best possible data quality. 2,107 micrographs showing Thon rings beyond 3.5 Å were used. The drifts of movie frames were corrected using MotionCor2. Magnification anisotropy was corrected with mag_distortion_estimate and mag_distortion_correct. CTFFIND4 was used to determine the contrast transfer function.Subsequently, a total of 268,364 particles were extracted and subjected to reference-f […]

call_split

Ensemble cryo EM elucidates the mechanism of translation fidelity

2017
Nature
PMCID: 5657493
PMID: 28538735
DOI: 10.1038/nature22397
call_split See protocol

[…] as follows. Videos were processed using IMOD to decompress frames and apply the gain reference. Videos were drift-corrected using unblur. Magnification anisotropy of the video sums was corrected with mag_distortion_estimate and mag_distortion_correct. CTFFIND3 was used to determine defocus values. Particles were automatically picked from 10×-binned images using Signature with a ribosome reference […]

library_books

Structure of RNA polymerase bound to ribosomal 30S subunit

2017
eLife
PMCID: 5655137
PMID: 29027901
DOI: 10.7554/eLife.28560.031

[…] processed using IMOD (RRID:SCR_003297) () to decompress frames and apply the gain reference. Movies were drift-corrected using unblur (). Magnification anisotropy of the movie sums was corrected with mag_distortion_estimate and mag_distortion_correct (). CTFFIND4 () was used to determine defocus values. 416 movies of 30S•RNAP complex (199 movies of 30SΔS1•RNAP complex) with high drift, low signal, […]

call_split

Ribosome•RelA structures reveal the mechanism of stringent response activation

2016
eLife
PMCID: 4974054
PMID: 27434674
DOI: 10.7554/eLife.17029.043
call_split See protocol

[…] essed using IMOD () to decompress frames and apply the gain reference. Movies were drift-corrected and exposure-filtered using unblur (). Magnification anisotropy of the movie sums was corrected with mag_distortion_estimate and mag_distortion_correct (). CTFFIND3 () was used to determine defocus values. 2233 movies from the first dataset and 207 movies from the second dataset with high drift, low […]

library_books

Structure and conformational states of the bovine mitochondrial ATP synthase by cryo EM

2015
eLife
PMCID: 4718723
PMID: 26439008
DOI: 10.7554/eLife.10180.049

[…] Magnification anisotropy () under the conditions described above was measured previously from images of a standard cross-grating specimen with the program mag_distortion_estimate (). The linear scaling parameters were 0.986 and 1.013, the azimuth of the distortion was 134.0°, and the program mag_distortion_correct was used to correct for this distortion […]


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mag_distortion_estimate institution(s)
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA

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