Dynamo protocols

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Dynamo specifications

Information


Unique identifier OMICS_15595
Name Dynamo
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages MATLAB
Computer skills Medium
Stability Stable
Maintained Yes

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  • person_outline Daniel Castano-Diez <>

Publications for Dynamo

Dynamo in pipelines

 (3)
2017
PMCID: 5376648
PMID: 28332496
DOI: 10.1038/ncomms14813

[…] 200 pixel × 200 pixel × 80 pixel volumes. volumes were prealigned with spider, using as reference the 3d map of the trichonympha sp. cartwheel the prealigned boxes were subsequently re-aligned with dynamo, using the same reference. an average was performed on the aligned boxes, and the average symmetrized to obtain a faithful compound structure of the cartwheel. note that subtomogram averaging […]

2016
PMCID: 4858563
PMID: 27117403
DOI: 10.1016/j.celrep.2016.03.082

[…] function parameters were estimated and images corrected by phase flipping (). further 2× binning was applied, resulting in the final pixel size of 2.7 å., sub-tomogram averaging was carried out in dynamo () using a previously determined structure of the tulv spike (emdb: 1704) as an initial template and following an iterative gold-standard alignment strategy (, ). to reduce template bias, […]

2015
PMCID: 4682100
PMID: 26656452
DOI: 10.1038/ncomms10114

[…] filtering was applied to tomograms for sub-tomogram identification and selection., sub-tomogram positions were manually selected in imod and extracted from raw tomograms using the dtcrop function in dynamo. initial alignment was performed manually with the dynamo gallery. further sub-tomogram alignment and averaging was conducted in dynamo with a modification of splitting particles into two […]

Dynamo in publications

 (11)
PMCID: 5783950
PMID: 29367607
DOI: 10.1038/s41467-017-02789-2

[…] gctf. the estimated defocus was used to correct the ctf of the dose-weighted tilt series by ctfphaseflip in imod using strip width of 20 pixels. tomograms were reconstructed by imod, managed in dynamo catalogue and binned by a factor of 2 resulting in the final pixel size of 2.7 å/pixel. a total of 120 rvfv virions at ph 7.5 and 30 virions at ph 5.0 were picked and extracted into boxes […]

PMCID: 5714281
PMID: 29144446
DOI: 10.1038/nature24490

[…] local fsc plots were used for local low pass filtering, figure of merit weighting, and sharpening., resolution was also estimated for each protein layer using three cylindrical fsc masks made in the dynamo software package (). the circular cross section of each masks contained a full nc subunit; i.e. two nps, two vp24s, and the unassigned densities. the three masks had varying heights […]

PMCID: 5516000
PMID: 28781998
DOI: 10.1007/s41048-017-0040-0

[…] the surge of open-access software for spt, such as av3 (förster and hegerl ), peet (nicastro et al. ) (available through imod (kremer et al. )), jsubtomo (huiskonen et al. ), pytom (hrabe et al. ), dynamo (castaño-díez et al. ), eman2 (galaz et al. ; murray et al. ; galaz-montoya et al. ), and relion (bharat et al. )., the evolution of cryoet can be followed through reviews in this discipline […]

PMCID: 5376648
PMID: 28332496
DOI: 10.1038/ncomms14813

[…] 200 pixel × 200 pixel × 80 pixel volumes. volumes were prealigned with spider, using as reference the 3d map of the trichonympha sp. cartwheel the prealigned boxes were subsequently re-aligned with dynamo, using the same reference. an average was performed on the aligned boxes, and the average symmetrized to obtain a faithful compound structure of the cartwheel. note that subtomogram averaging […]

PMCID: 5482573
PMID: 28621666
DOI: 10.7554/eLife.26691.069

[…] was performed in imod. subtomograms were extracted from the surface of the vesicles. subtomogram averaging was performed using scripts derived from the tom and av3 software packages (; ) and dynamo (). each dataset was split into two halves, each half including odd- and even-numbered vesicles. the copi triad structure (emdb-2985, []) was low pass filtered to 55 å and used for the initial […]

Dynamo funding source(s)
This work was in part supported by the Swiss Initiative for Systems Biology SystemsX.ch (RTD CINA) and by the Swiss National Science Foundation (NCCR Transcure and grant 205320_144427).

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