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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

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