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• 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
• 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) - 11:26, 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) - 17:03, 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) - 09:22, 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) - 13:09, 18 September 2017
• 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
• 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) - 09:50, 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) - 10:24, 1 June 2016
• 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) - 14:31, 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) - 11:55, 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) - 16:17, 13 September 2021
• 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) - 19:27, 3 September 2021
• 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) - 14:49, 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) - 14:13, 18 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 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 (3,161 words) - 00:05, 6 August 2021
• 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) - 17:54, 26 October 2017
• Pasteur workshop 2017
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  2 KB (304 words) - 11:09, 19 July 2017
• Postprocessing plugins
  ...action that ''Dynamo'' will execute after each iteration during a project alignment.
  7 KB (1,043 words) - 19:07, 9 March 2017
• Principal component analysis
  ...icles. Thus, you need a [[data folder]] and a [[table]] that describes the alignment.
  3 KB (424 words) - 19:03, 28 March 2020
• Oblique slices in tomoslice
  :-Alignment of axes in orthogonal orientations
  3 KB (423 words) - 17:23, 27 April 2017
• Hints for purchase of computing resources
  ...aging, some steps in [[PCA]] analysis, manual management of models. Even [[alignment project]]s with modest number of particles can be reasonably executed on a ...tion, cropping particles, and any preprocessing related to the creation of alignment project. Once the project has been created (as a folder and an execution sc
  6 KB (966 words) - 15:34, 24 January 2022
• Walkthrough on adaptive bandpass filtering
  Masks are initiated to default values. This means spherical masks for alignment and classification masks, and full cubes for smoothing and fourier mask of Then select the number of available cores for alignment and averaging.
  10 KB (1,461 words) - 20:12, 27 November 2017
• Starters guide
  ...describes the basics including particle picking, initial model generation, alignment, averaging and classification or particles. ''Dynamo'' has a standalone to ...:StartersGuideParticlesUnaligned.png|thumb|center|400px| Particles without alignment (<tt>table</tt> is switched off).]]
  24 KB (3,775 words) - 16:39, 6 September 2021
• EMBO workshop 2018
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  3 KB (397 words) - 09:01, 5 September 2018
• Tips for management of tomographic data sets
  ...rder to make easy to keep track on the processing steps already performed (alignment, reconstruction), the location of the intermediate results, and their bindi In this example, we assume that you are using <tt>imod</tt> for tomographic alignment and reconstruction of each tilt series. The raw data is stored in a tree be
  8 KB (1,277 words) - 19:14, 16 May 2017
• Cropping unbinned particles after having worked with binned particles
  ...to ease computations, a binning order is passed to the [[Alignment project|alignment]] or classification project.
  8 KB (1,292 words) - 18:50, 6 February 2020
• Indicating the missing wedge
  ...will depend on the reconstruction program you used, and how it handled the alignment. Lets assume a <tt>ftype</tt> 1 (i.e., column 13 of table will be one). In
  3 KB (548 words) - 12:41, 3 April 2020
• Installation
  This shell is "activated" and can then be used to run [[alignment project]]s or to initiate an interactive session using the ''Dynamo'' [[Dyn
  3 KB (551 words) - 15:01, 22 June 2018
• Considerations for tomogram positioning in IMOD
  ...step and set the "Angle offset" and "Z shift" to zero. 2) Go to the "Fine Alignment" step and set the two values to zero too. Do ''not'' go back to the "Tomogr
  4 KB (646 words) - 15:34, 9 April 2019
• Walkthrough for lattices on vesicles
  ...n be used directly by ''Dynamo'' to operate an extraction and a subsequent alignment. ...s that are poorly defined still have a chance to get driven by a posterior alignment to the center of the box. If we initialize some variables:
  18 KB (3,099 words) - 14:19, 18 August 2021
• San Diego Workshop 2018
  ...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)
  13 KB (1,774 words) - 19:58, 26 January 2018
• Walkthrough on PCA through the command line
  ...than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a table that expreses the alignment
  14 KB (1,969 words) - 23:58, 8 February 2021
• Walkthrough for template matching
  === Through manual alignment === ====Manual alignment of some particles ====
  25 KB (3,943 words) - 14:11, 18 August 2021
• Walkthrough on localized reconstruction
  ...b>sc</sub>'' and determined by the rotation axis implicitly defined by the alignment. Now, we could find the actual positions of the gold beads with an alignment project. We create a spherical template and mask:
  17 KB (2,770 words) - 11:57, 27 August 2018
• Computers Basel 2016
  #run your alignment by typing <tt>srun my_project.exe</tt>
  5 KB (815 words) - 16:20, 24 August 2017
• Computers Basel 2017
  # Create alignment project >> computational parameters >> system_gpu
  5 KB (843 words) - 12:23, 25 August 2017
• Practicals Birkbeck 2019
  [ 2 ] marked for alignment: 22 == Project for rotational alignment ==
  37 KB (5,792 words) - 20:30, 2 September 2019
• Framework for estimation of membrane thickness
  This framework is more useful in plastic sections. The premise is that an [[alignment project]] has been created to fix the position an orientation of a set of p
  5 KB (800 words) - 12:09, 9 May 2017
• Dynamo workshop 2017
  * Creation of alignment projects.
  4 KB (649 words) - 10:05, 27 August 2017
• Advanced starters guide (EMBO2021)
  [ 2 ] marked for alignment: 22 ...the ''standalone'' option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue box). See the [[EMBO_w
  46 KB (7,267 words) - 12:09, 13 September 2021
• Walkthrough on creation of 3d scenes
  * Proteins located in the tomogram, with the orientations provided during the alignment. we recover our table with locations '''and'' alignment parameters
  13 KB (2,062 words) - 12:46, 29 November 2017
• Advanced starters guide
  [ 2 ] marked for alignment: 22 ...the [[standalone]] option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue box) .
  47 KB (7,432 words) - 18:41, 3 September 2021
• GPUs EMBO 2016
  #run your alignment by typing <tt>srun dynamo_execute_project my_project</tt>
  6 KB (1,053 words) - 09:58, 31 August 2016
• Construction of masks
  ...amo'' for several purposes: indicating the active part of the template for alignment, restricting the area of the aligned particles that will count for classifi
  6 KB (943 words) - 11:58, 14 September 2017
• Standalone
  ...ch "core" will be handled by a different openMP process. You can also run alignment projects in the GPU, in which case you also have to mark the set of [[GPU i
  7 KB (1,143 words) - 15:56, 4 May 2018
• Particle extraction
  ...the metadata. Data folder and table can directly be used for [[subtomogram alignment]]
  7 KB (1,221 words) - 16:46, 24 April 2018
• Delft Workshop 2017
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  8 KB (1,246 words) - 13:51, 31 August 2017

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