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• Data folder
  ...lder is the minimal input that the [[dcp GUI]] needs in order to create an alignment project. ...{{t|myData}} can then be used as {{t|data folder}} parameter when creating alignment and classification projects,
  4 KB (637 words) - 17:48, 30 September 2019
• GPUs Basel 2018
  The main idea is that we create an alignment project locally, move it to the cluster on sciCORE and then run it using a ...ith 128 particles in the directory <code>myParticles</code> and a tutorial alignment project <code>myProject</code>.
  4 KB (691 words) - 15:22, 27 August 2018
• Integration with Warp and M
  * automated fiducial based tilt-series alignment ...ew [[Walkthrough on command line based tilt series alignment | tilt series alignment tools]]
  6 KB (992 words) - 13:47, 19 August 2020
• Example data sets
  Want to design and alignment problem? Here are some tips:
  885 bytes (127 words) - 18:34, 2 May 2016
• GPU
  ==Using the GPU in an alignment project== ...ltireference alignment inherits the "GPU-friendliness" of single reference alignment: the cc of many rotations of the template against the particle can be compu
  5 KB (902 words) - 08:44, 2 September 2016
• Practical Suggestions for Tomographic Reconstruction
  === Tilt series alignment === ...rations_for_tilt_series_alignment_in_IMOD | considerations for tilt series alignment]] with [https://bio3d.colorado.edu/imod/ IMOD].
  5 KB (871 words) - 15:59, 30 April 2019
• Getting started
  ...g]] tomograms, [[Particle extraction|extracting particles]], [[Subtomogram alignment|aligning]], averaging and [[Classification|classifying]] subtomograms, and
  943 bytes (119 words) - 11:08, 26 February 2021
• Cross correlation matrix
  #: alignment parameters A_i and A_j ...mal input is a set of particles (formatted as a [[data folder]]) and their alignment parameters (formatted as a [[table]]). You also may want to specify a class
  3 KB (471 words) - 12:16, 19 April 2016
• Materials Basel 2017
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Some tools for tilt series alignment, reconstruction, CTF correction.
  4 KB (538 words) - 09:58, 25 August 2017
• Pipelines for Workshop Heidelberg 2018
  * Alignment of tilt series with ''Dynamo'' * Independent alignment and resolution determination.
  7 KB (1,014 words) - 10:27, 22 August 2018
• 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
• EMBO workshop 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 (944 words) - 11:26, 6 September 2019
• Dynamo Matlab version
  The exception is the Parallel Computing Toolbox: if you want to execute alignment projects inside Matlab using several cores, then you need to buy a license
  1 KB (224 words) - 17:03, 20 April 2017
• Table convention
  2 : aligned value 1: marks the particle for alignment ...particles in the [[data folder]] that you don't want to included into the alignment or classification project. Of course, you can just a table that does not in
  6 KB (809 words) - 09:22, 25 November 2019
• MPI Cluster
  ''Dynamo'' can be run as [[standalone]] on a cluster of CPUs. This works for alignment and classification projects. Using the ''Dynamo'' standalone in a CPU clus ...can however be a problem when you have several thousands particles and the alignment step only covers a few Euler triplets.
  8 KB (1,287 words) - 13:09, 18 September 2017
• Walkthrough on command line based tilt series alignment
  ...sed mode. The [[Walkthrough on GUI based tilt series alignment | GUI based alignment walkthrough]] shows how to operate this procedure through the GUI. Here, we The following commands create a new alignment workflow in a separate folder. Make sure ''Dynamo'' is running and type the
  12 KB (1,823 words) - 12:15, 11 August 2021
• Prato Workshop 2019
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...[[adaptive bandpass filtering]], a way of conducting a ''golden standard'' alignment procedure . (~40 mins)
  6 KB (794 words) - 09:50, 4 April 2019
• Video tutorials
  ...://youtu.be/SWKyHrLETPQ youtube link]] shows an introduction to setting up alignment projects in ''Dynamo''. It works on the old {{t|dynamo_project_manager}} GU
  1 KB (226 words) - 10:24, 1 June 2016
• Prato Workshop 2018
  General operation of the GUI that creates alignment projects. ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  7 KB (984 words) - 14:31, 12 April 2018
• Diamond Workshop 2017
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...[[adaptive bandpass filtering]], a way of conducting a ''golden standard'' alignment procedure . (~40 mins)
  6 KB (845 words) - 11:55, 7 December 2017
• Starters guide (EMBO2021)
  =Subtomogram alignment and averaging= ...eed an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particl
  15 KB (2,422 words) - 16:17, 13 September 2021
• Starters guide (workshop version)
  =Subtomogram alignment and averaging= ...eed an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particl
  15 KB (2,427 words) - 19:27, 3 September 2021
• Cropping table
  ...is always useful to use the produced {{t|crop.tbl}} table to initialize an alignment project, as it contains the identities of the particles actually on the dat ...6. Including the shifts is crucial if the table expresses the result of an alignment project, as the final ''xyz'' position of the particles will be the additio
  5 KB (787 words) - 14:49, 23 May 2018
• Getting a Structure from Multiple Tomograms of HIV Capsids (walkthrough)
  ...e tomograms through the ''Dynamo'' catalogue and developing strategies for alignment projects to reach a reasonable structure from a set of tomograms. You will ...crop points and their orientations (when visualizing actual results of an alignment project use option '' 'corrected_oriented_positions'' ' instead of the one
  22 KB (3,572 words) - 14:13, 18 August 2021
• Walkthrough on GUI based tilt series alignment (EMBO2021)
  ...ased tilt series alignment | walkthrough on command line based tilt series alignment]] shows how to operate this procedure through the command line. = Creating an alignment workflow=
  21 KB (3,158 words) - 17:09, 6 September 2021
• Walkthrough on GUI based tilt series alignment
  ...ased tilt series alignment | walkthrough on command line based tilt series alignment]] shows how to operate this procedure through the command line. = Creating an alignment workflow=
  21 KB (3,161 words) - 00:05, 6 August 2021
• Subboxing
  ...subunits of interest with relation to the center of the average. Then, the alignment [[table]] that produced the average can be used to produce a ''subboxed tab
  2 KB (374 words) - 17:54, 26 October 2017
• Pasteur workshop 2017
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  2 KB (304 words) - 11:09, 19 July 2017
• Postprocessing plugins
  ...action that ''Dynamo'' will execute after each iteration during a project alignment.
  7 KB (1,043 words) - 19:07, 9 March 2017
• Principal component analysis
  ...icles. Thus, you need a [[data folder]] and a [[table]] that describes the alignment.
  3 KB (424 words) - 19:03, 28 March 2020
• Oblique slices in tomoslice
  :-Alignment of axes in orthogonal orientations
  3 KB (423 words) - 17:23, 27 April 2017

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