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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 citations

 (12)
library_books

Shielding and activation of a viral membrane fusion protein

2018
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 […]

library_books

Structure and assembly of the Ebola virus nucleocapsid

2017
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 […]

library_books

The advent of structural biology in situ by single particle cryo electron tomography

2017
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 […]

library_books

Cell free reconstitution reveals centriole cartwheel assembly mechanisms

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 […]

library_books

9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments

2017
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 […]

library_books

Cryo electron tomography reveals novel features of a viral RNA replication compartment

2017
PMCID: 5515581
PMID: 28653620
DOI: 10.7554/eLife.25940.022

[…] researcher using the particle estimation for electron tomography (peet) set of programs from the imod tomography suite (; rrid_scr_003297) without prior knowledge of the results obtained using dynamo. the independent dynamo and peet subtomogram reconstructions revealed essentially identical structures, providing assurance of negligible unintentional error or bias., this paper was supported […]


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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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