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• 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
• 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 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) - 18:06, 6 September 2021

Page text matches

• 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) - 10:36, 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) - 15:53, 19 May 2016
• Classification
  ...]] is more time consuming, but it performs simultaneous classification and alignment.
  379 bytes (49 words) - 12:47, 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) - 18:06, 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) - 15:17, 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) - 10:37, 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) - 12:39, 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) - 16:09, 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) - 23:57, 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) - 19:41, 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) - 18:09, 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) - 09:10, 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) - 18:06, 6 September 2021
• Helical symmetry
  == Using symmetrization in alignment projects==
  3 KB (429 words) - 15:32, 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) - 22:43, 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) - 15:16, 27 August 2020
• Particle picking
  ...a single [[data folder]] that can be used to design an [[alignment project|alignment project]]
  2 KB (340 words) - 13:31, 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) - 13:10, 19 April 2016
• 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) - 11:05, 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) - 12:51, 27 August 2019
• 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

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