Search results

Create the page "Alignment" on this wiki! See also the search results found.

• 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

View (previous 50 | next 50) (20 | 50 | 100 | 250 | 500)