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• Computing environments
  ...on of tomograms]], and a dedicated computing system (GPUs or clusters) for alignment projects (where the most intensive number crunching occurs) During the alignment stage, [[data folder|cropped particles]] are stored in disk and read into
  2 KB (397 words) - 09:43, 29 April 2016
• Daverage
  ...sic command line option for averaging particles in a [[data folder]] using alignment parameters expresed inside a [[table]]. Particles and shifted, then rotated, following the alignment parameters in the table. By convention, positions 4:6 and 7:9 in a the <tt
  5 KB (792 words) - 15:09, 13 October 2017
• Materials Basel 2016
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Manual alignment.
  3 KB (413 words) - 11:12, 19 August 2016
• EMBO workshop 2016
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Manual alignment.
  3 KB (404 words) - 17:51, 31 August 2016
• Dynamo Workshop CIC bioGUNE 2020
  ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir * Alignment and reconstruction of tilt series.
  4 KB (570 words) - 18:01, 11 August 2020
• Workshop exercises
  == Alignment ==
  4 KB (698 words) - 10:30, 1 September 2016
• Basel Workshop 2019
  ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir * Alignment and reconstruction of tilt series.
  4 KB (662 words) - 12:07, 12 October 2021
• Fourier mask on template
  The Fourier Mask that you define on a template during an alignment project describes the Fourier content of the template, ''not'' the one of t
  1 KB (204 words) - 10:25, 6 July 2017
• Basel Dynamo Workshop 2018
  ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir * Alignment and reconstruction of tilt series.
  5 KB (673 words) - 15:26, 27 August 2018
• EMBO workshop 2021
  ...ht use this number later for tasks that require parallel processing (e.g., alignment projects): ...to quit ''Dynamo'' every time you want to do something else (e.g., running alignment projects or using chimera). Be aware that if you press ctrl+c within the ''
  6 KB (894 words) - 18:07, 11 September 2021
• Catalogue
  ...ding [[table]] that can be feed into a [[alignment project|project]] for [[alignment]] or [[classification]]. ...ed to define a catalogue. You already have all you need to start designing alignment projects.
  5 KB (855 words) - 22:28, 14 August 2017
• Particle File List
  This file can be used as input for <tt>average</tt> or an alignment project. You can use a <tt>table</tt> flag in order to pass a table. ...own 8 particles, and a table to refer them. This table contains the actual alignment parameters of the particles in the respective data folder.
  7 KB (1,151 words) - 13:01, 30 November 2020
• Table
  === Initial metadata for alignment projects === === Results of alignment iterations ===
  8 KB (1,191 words) - 09:50, 1 June 2017
• EMBO workshop 2020
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...o with Warp and M]] to be able to take advantage of Dynamo for tilt-series alignment and particle picking and plug the results into M's multi-particle refinemen
  9 KB (1,391 words) - 16:19, 25 August 2020
• Fourier compensation during averaging
  While rotating a cube, there is always a [[ Border alignment artifact | rotation artifact]] ...ngth. During execution of the project, the small particle will be used for alignment (to save time), and the ''container'' particles will be used for averaging
  4 KB (582 words) - 12:06, 21 November 2017
• Walkthrough on manual marker clicking
  ...ilt series alignment]] and [[Walkthrough on command line based tilt series alignment ]]. = Fitting to an alignment model =
  9 KB (1,526 words) - 20:10, 13 July 2021
• Programmatic control of alignment and reconstruction workflows
  Alignment and reconstruction workflows can be used with the GUI or on a totally progr Alignment and reconstruction workflow folders are marked with the extension <tt>.AWF<
  12 KB (1,917 words) - 18:35, 10 July 2019
• Pdf tutorials
  * in alignment projects {{pdftutorial|command_line_projects|link}}
  2 KB (208 words) - 13:19, 29 April 2016
• Dynamo Workshop at the International School of Crystallography 2019
  ...information on how to do it on each platform) that can be used to run [[alignment project]]s or to initiate an interactive session using the ''Dynamo'' [[Dyn ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  7 KB (929 words) - 15:17, 5 June 2019
• Fourier acceleration
  ...d by the [[Limiting shifts| shift limiting policy]] used in the particular alignment project. Even though Fourier acceleration is benefitial compared to direct
  2 KB (242 words) - 10:38, 18 April 2016

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