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• 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

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