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Page title matches

  • Alignment project
    [[Category: alignment]] [[Category: Alignment Project]]
    5 KB (793 words) - 07:41, 27 October 2017
  • Multireference alignment
    [[Category:Multireference Alignment]] In a multireference alignment [MRA] project, each particle will be aligned against R different templates.
    4 KB (592 words) - 20:58, 6 June 2018
  • Alignment mask
    [[Category:alignment project]] The ''alignment mask'' is use during alignment to define the part of the template cube that will actually be used to align
    3 KB (431 words) - 12:29, 15 April 2016
  • Symmetrization during alignment
    591 bytes (90 words) - 11:50, 20 February 2018
  • Subtomogram alignment
    [[Category:Alignment]] ...nment project]], which will run alignment and averaging in an [[iIterative alignment| iterative way]] in order to gradually improve the attained [[resolution]].
    674 bytes (101 words) - 17:02, 29 April 2016
  • Border alignment artifact
    760 bytes (102 words) - 07:33, 13 October 2017
  • Tilt series alignment workflow folder
    Remember to use the whole path if you are not in the alignment workflow folder. This file is normally generated by ''Dynamo'' when the alignment workflow is created. Note that these angles could also be stored in a diffe
    6 KB (945 words) - 16:06, 6 February 2019
  • 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 (3,180 words) - 11:39, 15 March 2024
  • Considerations for tilt series alignment in IMOD
    When doing the tilt series alignment in [https://bio3d.colorado.edu/imod/ IMOD], we strongly recommend to consid === Alignment parameters ===
    3 KB (471 words) - 10:57, 27 March 2019
  • 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) - 16:35, 10 July 2019
  • 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) - 15:09, 6 September 2021
  • 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
    13 KB (1,890 words) - 11:39, 15 March 2024
  • Walkthrough on GUI based tilt series alignment (EMBO2023)
    = Creating an alignment workflow= Start the alignment GUI by typing the command <tt>dtsa</tt> (short form of <tt>dynamo_tilt_seri
    21 KB (3,116 words) - 14:28, 8 September 2023
  • Walkthrough on command line based tilt series alignment (EMBO2021)
    ...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) - 16:06, 6 September 2021
  • Walkthrough on command line based tilt series alignment (EMBO2023)
    This last tutorial on tilt series alignment is command line based. When woking under high data regimes, it is, perhaps, The following commands create a new alignment workflow in a separate folder. So, as recommended before, make sure you iso
    6 KB (840 words) - 12:06, 9 September 2023
  • Walkthrough on GUI based tilt series alignment (SciLifeLab 2023)
    = Creating an alignment workflow= Start the alignment GUI by typing the command <tt>dtsa</tt> (short form of <tt>dynamo_tilt_seri
    20 KB (3,113 words) - 11:12, 20 October 2023
  • Walkthrough on GUI based tilt series alignment (Copenhagen 2024)
    = Creating an alignment workflow= Start the alignment GUI by typing the command <tt>dtsa</tt> (short form of <tt>dynamo_tilt_seri
    20 KB (3,113 words) - 18:05, 22 January 2024
  • Walkthrough on command line based tilt series alignment (SciLifeLab 2023)
    This last tutorial on tilt series alignment is command line based. When woking under high data regimes, it is, perhaps, The following commands create a new alignment workflow in a separate folder. So, as recommended before, make sure you iso
    5 KB (809 words) - 18:08, 22 January 2024
  • Walkthrough on command line based tilt series alignment (Copenhagen 2024)
    This last tutorial on tilt series alignment is command line based. When woking under high data regimes, it is, perhaps, The following commands create a new alignment workflow in a separate folder. So, as recommended before, make sure you iso
    5 KB (808 words) - 18:08, 22 January 2024

Page text matches

  • Subtomogram alignment
    [[Category:Alignment]] ...nment project]], which will run alignment and averaging in an [[iIterative alignment| iterative way]] in order to gradually improve the attained [[resolution]].
    674 bytes (101 words) - 17:02, 29 April 2016
  • Tomogram quality assessment
    ...ommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore a good tomogram reconstruction results in perfectly symmetric ...bead. In the Z-view, the beads show symmetric white "wings". Right: A bad alignment causes asymmetries and results in curved or distorted shapes in both views.
    1 KB (221 words) - 14:34, 31 January 2019
  • Multireference project
    #REDIRECT [[Multireference alignment]]
    38 bytes (3 words) - 09:29, 22 April 2016
  • Alignment mask
    [[Category:alignment project]] The ''alignment mask'' is use during alignment to define the part of the template cube that will actually be used to align
    3 KB (431 words) - 12:29, 15 April 2016
  • Considerations for tilt series alignment in IMOD
    When doing the tilt series alignment in [https://bio3d.colorado.edu/imod/ IMOD], we strongly recommend to consid === Alignment parameters ===
    3 KB (471 words) - 10:57, 27 March 2019
  • Refined table
    The ''refined table'' is the result of the alignment iteration. ''Dynamo'' produces one refined table per iteration and referenc ...icular, ''Dynamo'' should fill some columns in a ''refined table'' during alignment:
    2 KB (304 words) - 09:15, 22 April 2016
  • Alignment project
    [[Category: alignment]] [[Category: Alignment Project]]
    5 KB (793 words) - 07:41, 27 October 2017
  • Programmatic reconstruction of tomograms
    ...nment parameters, and to locate easily functionalities associated with the alignment of stacks. An important step is to establish the center of the alignment:
    3 KB (496 words) - 09:10, 3 July 2018
  • Multireference alignment
    [[Category:Multireference Alignment]] In a multireference alignment [MRA] project, each particle will be aligned against R different templates.
    4 KB (592 words) - 20:58, 6 June 2018
  • Seed oversampling
    == Oversampling in an alignment project == ...all this procedure ''trimming''). This can be done manually or through the alignment project.
    4 KB (683 words) - 11:51, 3 February 2017
  • Smoothing mask
    ...r one (in order to create a comparison), this average will have a [[border alignment artifact]] resulting from the rotation and shift. If no masking is used, th ...o be aligned to the other, which inevitably creates a sharp edge [[Border alignment artifact| artifact]] in one of the two averages. Applying the same mask on
    1 KB (191 words) - 08:36, 2 May 2016
  • Hints for improving a refinement
    ...ns is heterogeneity. If you are aligning two or more classes together, the alignment would get stuck at some point. If you are lucky, the average will be a sort ...A first approach to diagnose this is to check the cross correlation of the alignment (in column 10 of the [[table]]). A simple inspection of the histogram can
    5 KB (720 words) - 13:53, 19 May 2016
  • Classification
    ...]] is more time consuming, but it performs simultaneous classification and alignment.
    379 bytes (49 words) - 10:47, 22 March 2016
  • Tilt series alignment workflow folder
    Remember to use the whole path if you are not in the alignment workflow folder. This file is normally generated by ''Dynamo'' when the alignment workflow is created. Note that these angles could also be stored in a diffe
    6 KB (945 words) - 16:06, 6 February 2019
  • Materials Basel 2019
    ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. === Fiducial based alignment and reconstruction ===
    5 KB (698 words) - 13:17, 29 August 2019
  • Multireference Analysis
    Multireference analysis implements simultaneous alignment and classification. ...to have been correctly aligned in the first place. If heterogeneity drives alignment to fail, PCA may not be capable to classify the particles.
    1 KB (215 words) - 08:37, 19 August 2020
  • Resolution
    ...ost widespread ways of simultaneously measuring resolution and driving the alignment is the so called "golden standard" method. A version of this approach is av
    330 bytes (44 words) - 10:39, 14 April 2016
  • ''Dynamo''workshop at the New York Structural Biology Center 2016
    ==Introduction: alignment projects== ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
    3 KB (436 words) - 14:09, 9 December 2016
  • Dcp GUI
    ...(for Dynamo Current Project) is the main tool for interactive design of [[Alignment project| projects]]. The GUI follows the pipeline for designing an [[Alignment project]]. To create a new project, just write the name in the <tt>Project<
    3 KB (503 words) - 21:57, 13 September 2017
  • Table column convention
    Used when a table is fed into ''Dynamo''as initial table for an alignment project. Value 1 tells ''Dynamo'' that the particle is to be used during an alignment project, values 0 skips the particle.
    5 KB (721 words) - 17:41, 8 March 2018
  • Averaging of subtomograms
    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) - 16:09, 6 December 2017
  • Adaptive bandpass filtering
    [[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) - 07:10, 28 November 2017
  • Walkthrough on command line based tilt series alignment (EMBO2021)
    ...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) - 16:06, 6 September 2021
  • Helical symmetry
    == Using symmetrization in alignment projects==
    3 KB (429 words) - 13:32, 1 June 2016
  • Materials Basel 2018
    ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. === Alignment and reconstruction ===
    4 KB (604 words) - 20:43, 29 August 2018
  • Getting a Structure from Multiple Tomograms of HIV Capsids
    ...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) - 13:16, 27 August 2020
  • Downloads
    We are restructuring our modules for alignment of tilt series and classification. Next stable releases will come in winter * CTF hand check in automated tilt series alignment.
    4 KB (640 words) - 13:28, 30 August 2023
  • Walkthrough on command line based tilt series alignment (Copenhagen 2024)
    This last tutorial on tilt series alignment is command line based. When woking under high data regimes, it is, perhaps, The following commands create a new alignment workflow in a separate folder. So, as recommended before, make sure you iso
    5 KB (808 words) - 18:08, 22 January 2024
  • Walkthrough on command line based tilt series alignment (SciLifeLab 2023)
    This last tutorial on tilt series alignment is command line based. When woking under high data regimes, it is, perhaps, The following commands create a new alignment workflow in a separate folder. So, as recommended before, make sure you iso
    5 KB (809 words) - 18:08, 22 January 2024
  • Particle picking
    ...a single [[data folder]] that can be used to design an [[alignment project|alignment project]]
    2 KB (340 words) - 11:31, 23 February 2017
  • Why is GPU not available for classification?
    ...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) - 11:10, 19 April 2016
  • Walkthrough on command line based tilt series alignment (EMBO2023)
    This last tutorial on tilt series alignment is command line based. When woking under high data regimes, it is, perhaps, The following commands create a new alignment workflow in a separate folder. So, as recommended before, make sure you iso
    6 KB (840 words) - 12:06, 9 September 2023
  • Scripted creation of a project in the Linux command line
    ...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) - 09:05, 22 September 2016
  • GPUs Basel 2019
    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) - 10:51, 27 August 2019
  • Main Page
    ...to [[Particle picking|pick particles]] and create [[Subtomogram alignment|alignment]] and [[Classification |classification projects]] to be run on different [
    2 KB (279 words) - 07:13, 29 March 2022
  • 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) - 15:48, 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) - 13:22, 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) - 11:47, 19 August 2020
  • Example data sets
    Want to design and alignment problem? Here are some tips:
    885 bytes (127 words) - 16:34, 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) - 06:44, 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) - 13:59, 30 April 2019
  • PSI Workshop 2023
    ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir | 6a || 11:30 - 12:00 || [[Walkthrough on manual marker clicking | Alignment of tilt series: Manual]]
    5 KB (685 words) - 06:55, 6 October 2023
  • SciLife Lab Workshop for Subtomogram Averaging 2023
    ...o</it> implements to tackle them. We will thus discuss different tools for alignment of tilt series, creation of tomograms, location of particles and design of | [[Walkthrough_on_GUI_based_tilt_series_alignment_(EMBO2021)| Tilt series alignment with GUI]]
    4 KB (501 words) - 14:32, 19 October 2023
  • Getting started
    ...g]] tomograms, [[Particle extraction|extracting particles]], [[Subtomogram alignment|aligning]], averaging and [[Classification|classifying]] subtomograms, and
    932 bytes (117 words) - 12:08, 16 August 2023
  • Cross correlation matrix
    #: 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) - 10:16, 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) - 07:58, 25 August 2017
  • Pipelines for Workshop Heidelberg 2018
    * Alignment of tilt series with ''Dynamo'' * Independent alignment and resolution determination.
    7 KB (1,014 words) - 08:27, 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) - 07:43, 29 April 2016
  • Copenhagen Workshop on Cryo Electron Tomography 2024
    ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir | Alignment of tilt series || https://drive.google.com/drive/folders/1VPYk91xJ6cLCSy6Mg
    8 KB (1,029 words) - 14:32, 7 February 2024
  • 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) - 13:09, 13 October 2017
  • Materials Basel 2016
    ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Manual alignment.
    3 KB (413 words) - 09:12, 19 August 2016
  • EMBO workshop 2016
    ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Manual alignment.
    3 KB (404 words) - 15:51, 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) - 16:01, 11 August 2020
  • EMBO workshop 2023
    | [[Walkthrough on manual marker clicking (EMBO2023) | Alignment of tilt series: Manual]] | [[Walkthrough on GUI based tilt series alignment (EMBO2023)| Tilt series alignment with GUI]]
    5 KB (748 words) - 12:28, 10 September 2023
  • Göttingen Workshop 2024
    ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir | Alignment of tilt series || https://drive.google.com/drive/folders/1VPYk91xJ6cLCSy6Mg
    7 KB (1,016 words) - 14:01, 12 April 2024
  • Workshop exercises
    == Alignment ==
    4 KB (698 words) - 08:30, 1 September 2016
  • SciLifeLab Workshop for Cryo Electron Tomography Processing
    ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir ...1:45 - 12:30 || [[Walkthrough on manual marker clicking (SciLifeLab 2023)| Alignment of tilt series: Manual]]
    6 KB (807 words) - 06:47, 27 October 2023
  • 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) - 10:07, 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) - 08:25, 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) - 13:26, 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) - 16:07, 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) - 20:28, 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) - 12:30, 6 February 2023
  • Table
    === Initial metadata for alignment projects === === Results of alignment iterations ===
    8 KB (1,191 words) - 07:50, 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) - 14:19, 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) - 10:06, 21 November 2017
  • 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) - 16:35, 10 July 2019
  • Pdf tutorials
    * in alignment projects {{pdftutorial|command_line_projects|link}}
    2 KB (208 words) - 11:19, 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) - 13:17, 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) - 08:38, 18 April 2016
  • Walkthrough on manual marker clicking
    ...ilt series alignment]] and [[Walkthrough on command line based tilt series alignment ]]. = Fitting to an alignment model =
    10 KB (1,577 words) - 11:42, 15 March 2024
  • 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) - 09:26, 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) - 15:03, 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) - 07:22, 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) - 11:09, 18 September 2017
  • 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) - 07:50, 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) - 08:24, 1 June 2016
  • 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
    13 KB (1,890 words) - 11:39, 15 March 2024
  • 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) - 12:31, 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) - 09:55, 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) - 14:17, 13 September 2021
  • Starters guide (EMBO2023)
    =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) - 14:56, 8 September 2023
  • 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) - 17:27, 3 September 2021
  • Starters guide (Copenhagen 2024)
    =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) - 12:26, 25 January 2024
  • Starters guide (Göttingen 2024)
    =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) - 11:19, 8 April 2024
  • Starters guide (SciLifeLab 2023)
    =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 (2,424 words) - 14:17, 25 October 2023
  • 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) - 12:49, 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) - 12:13, 18 August 2021
  • Getting a Structure from Multiple Tomograms of HIV Capsids (Copenhagen 2024)
    ...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 (3,560 words) - 15:37, 22 January 2024
  • Getting a Structure from Multiple Tomograms of HIV Capsids (EMBO2023)
    ...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 (3,583 words) - 16:27, 8 September 2023
  • 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) - 15:09, 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 (3,180 words) - 11:39, 15 March 2024
  • Walkthrough on GUI based tilt series alignment (SciLifeLab 2023)
    = Creating an alignment workflow= Start the alignment GUI by typing the command <tt>dtsa</tt> (short form of <tt>dynamo_tilt_seri
    20 KB (3,113 words) - 11:12, 20 October 2023
  • Walkthrough on GUI based tilt series alignment (Copenhagen 2024)
    = Creating an alignment workflow= Start the alignment GUI by typing the command <tt>dtsa</tt> (short form of <tt>dynamo_tilt_seri
    20 KB (3,113 words) - 18:05, 22 January 2024
  • Walkthrough on GUI based tilt series alignment (EMBO2023)
    = Creating an alignment workflow= Start the alignment GUI by typing the command <tt>dtsa</tt> (short form of <tt>dynamo_tilt_seri
    21 KB (3,116 words) - 14:28, 8 September 2023
  • Walkthrough on manual marker clicking (SciLifeLab 2023)
    ...escribes the tools to ''manually'' locate fiducial markers for tilt series alignment using different graphical tools. = Fitting to an alignment model =
    9 KB (1,536 words) - 10:17, 26 October 2023
  • Walkthrough on manual marker clicking (Copenhagen 2024)
    ...escribes the tools to ''manually'' locate fiducial markers for tilt series alignment using different graphical tools. = Fitting to an alignment model =
    9 KB (1,536 words) - 18:04, 22 January 2024
  • Walkthrough on manual marker clicking (EMBO2023)
    ...escribes the tools to ''manually'' locate fiducial markers for tilt series alignment using different graphical tools. = Fitting to an alignment model =
    10 KB (1,554 words) - 12:10, 9 September 2023
  • Neighborhood analysis
    ...ed in Dynamo as a function that analyses particles through their [[table | alignment table]]. ...distance is measured in pixels between the centers of the particles after alignment. The default value is 5 pixels. This value should be kept reasonably small,
    6 KB (972 words) - 11:51, 29 April 2024
  • 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) - 15:54, 26 October 2017

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