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  • Averaging of subtomograms means applying an available set of alignment parameters onto a set of data particles and adding them together. Because ...particle outside an interior sphere will be discarded to minimize [[Border alignment artifact | rotation artifacts]] <br />- default value is 1.
    5 KB (818 words) - 17:09, 6 December 2017
  • [[Category: Multireference alignment‏‎]] The "golden standard" methodology is a widespread method to drive the alignment process avoiding overfitting and providing an accepted estimation of the at
    4 KB (666 words) - 08:10, 28 November 2017
  • ...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 loaded and running (
    6 KB (875 words) - 17:06, 6 September 2021
  • == Using symmetrization in alignment projects==
    3 KB (429 words) - 14:32, 1 June 2016
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. === Alignment and reconstruction ===
    4 KB (604 words) - 21:43, 29 August 2018
  • ...tomograms through the Dynamo catalogue and to develop good strategies for alignment projects to reach a reasonable structure from a set of tomograms. This is a ...s used in the tutorial (adapted to the different pixelsize) for your first alignment projects.
    3 KB (489 words) - 14:16, 27 August 2020
  • ...a single [[data folder]] that can be used to design an [[alignment project|alignment project]]
    2 KB (340 words) - 12:31, 23 February 2017
  • ...onto the same piece of data. This is an optimal situation for direct space alignment, where the same template is rotated many times and compared to a given part
    715 bytes (111 words) - 12:10, 19 April 2016
  • ...older]], a [[table]],a template, and several masks (for [[Alignment mask|alignment]], classification, description of fourier content of template and [[Smoothi
    2 KB (400 words) - 10:05, 22 September 2016
  • The main idea is to create an alignment project on your local machine, move it to the sciCORE cluster and then run ...ith 128 particles in the directory <code>myParticles</code> and a tutorial alignment project <code>myProject</code>.
    4 KB (740 words) - 11:51, 27 August 2019
  • ...to [[Particle picking|pick particles]] and create [[Subtomogram alignment|alignment]] and [[Classification |classification projects]] to be run on different [
    2 KB (279 words) - 16:40, 6 September 2021
  • ...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) - 16:48, 30 September 2019
  • 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) - 14:22, 27 August 2018
  • * automated fiducial based tilt-series alignment ...ew [[Walkthrough on command line based tilt series alignment | tilt series alignment tools]]
    6 KB (992 words) - 12:47, 19 August 2020
  • Want to design and alignment problem? Here are some tips:
    885 bytes (127 words) - 17:34, 2 May 2016
  • ==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) - 07:44, 2 September 2016
  • === 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) - 14:59, 30 April 2019
  • ...g]] tomograms, [[Particle extraction|extracting particles]], [[Subtomogram alignment|aligning]], averaging and [[Classification|classifying]] subtomograms, and
    943 bytes (119 words) - 10:08, 26 February 2021
  • #: alignment parameters A<sub>i</sub> and A<sub>j</sub> ...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) - 11:16, 19 April 2016
  • ...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) - 08:58, 25 August 2017
  • * Enhanced tools for manual alignment of tilt series through fiducial markers. * tilt series alignment: improved reload of workflows, allows selection of reconstruction height
    4 KB (558 words) - 10:07, 27 August 2021
  • * Alignment of tilt series with ''Dynamo'' * Independent alignment and resolution determination.
    7 KB (1,014 words) - 09:27, 22 August 2018
  • ...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) - 08:43, 29 April 2016
  • ...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) - 14:09, 13 October 2017
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Manual alignment.
    3 KB (413 words) - 10:12, 19 August 2016
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Manual alignment.
    3 KB (404 words) - 16:51, 31 August 2016
  • ...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) - 17:01, 11 August 2020
  • == Alignment ==
    4 KB (698 words) - 09:30, 1 September 2016
  • ...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) - 11:07, 12 October 2021
  • 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) - 09:25, 6 July 2017
  • ...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) - 14:26, 27 August 2018
  • ...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) - 17:07, 11 September 2021
  • ...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) - 21:28, 14 August 2017
  • 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) - 12:01, 30 November 2020
  • === Initial metadata for alignment projects === === Results of alignment iterations ===
    8 KB (1,191 words) - 08:50, 1 June 2017
  • ...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) - 15:19, 25 August 2020
  • 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) - 11:06, 21 November 2017
  • ...ilt series alignment]] and [[Walkthrough on command line based tilt series alignment ]]. = Fitting to an alignment model =
    9 KB (1,526 words) - 19:10, 13 July 2021
  • 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) - 17:35, 10 July 2019
  • * in alignment projects {{pdftutorial|command_line_projects|link}}
    2 KB (208 words) - 12:19, 29 April 2016
  • ...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) - 14:17, 5 June 2019
  • ...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) - 09:38, 18 April 2016
  • ...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) - 10:26, 6 September 2019
  • 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) - 16:03, 20 April 2017
  • 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) - 08:22, 25 November 2019
  • ''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) - 12:09, 18 September 2017
  • ...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) - 11:15, 11 August 2021
  • ...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) - 08:50, 4 April 2019
  • ...://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) - 09:24, 1 June 2016
  • 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) - 13:31, 12 April 2018

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