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• Angular search
  ...plate is rotated several times, and each rotated copy is compared with the particle. ...rticles. The last one, <tt>old_angles</tt> is obviously different for each particle, and in runtime is read from the table (provided by the user or [[Refined t
  3 KB (432 words) - 08:56, 2 May 2016
• Table column convention
  ...e significance of each column in a [[table]]. Each row represents a single particle. Identifies the particle number, so that each particle in the [[data folder]] indexed by the table is identified.
  5 KB (721 words) - 18:41, 8 March 2018
• Workshop exercises
  * Based on the particle tag (i.e., extract a subtable indexing only particles in a range of tags). == Particle extraction==
  4 KB (698 words) - 09:30, 1 September 2016
• Principal component analysis
  ...ticle can be represented by the contributions of each "eigenvolume" to the particle, i.e., by a set of "eigencomponents", normally in a number no much higher t ...(although much less intensive than the computation of the ccmatrix). Each particle is compared to each eigenvolume.
  3 KB (424 words) - 18:03, 28 March 2020
• Refined table
  * columns 3 (marks if the particle was actually used for the average produced at the iteration) * column 10 10 (the cross correlation coefficient computed for the alignment particle)
  2 KB (304 words) - 10:15, 22 April 2016
• Spectral averages in PCA
  ...is frequently frustrating not to detect a clear trend in the histograms of particle [[eigencomponents]]. Nevertheless, you might still manage to identify salie ...ting each eigenvolume separately, computing a weight as the average of all particle eigencomponents for that eigenvolume together. Then all the so weighted eig
  2 KB (351 words) - 14:53, 26 May 2016
• Framework for estimation of membrane thickness
  ...to get an estimation on the distance between the membrane layers on each ''particle''. This task can be performed through a [[multireference analysis]], but it gets the particle with tag 12 as a variable <tt>p</tt> in the workspace. You can also read al
  5 KB (800 words) - 11:09, 9 May 2017
• Multireference alignment
  In a multireference alignment [MRA] project, each particle will be aligned against R different templates. ...particles, each particle will be aligned against all the R references. The particle will produce R different cross-correlation scores and R different sets of a
  4 KB (592 words) - 21:58, 6 June 2018
• Multireference Analysis
  ...st match a given reference are used in the averaging step. Informally, the particle ''chooses'' which class it belongs to.
  1 KB (215 words) - 09:37, 19 August 2020
• Helical symmetry
  ==Symmetrizing a particle== Symmetrizing a helical particle can be done with the usual tool {{t|dsym}}:
  3 KB (429 words) - 14:32, 1 June 2016
• Table convention
  1 : tag tag of particle file in data folder 2 : aligned value 1: marks the particle for alignment
  6 KB (809 words) - 08:22, 25 November 2019
• Particle extraction
  Particle extraction is the process of using a set of positions (and possibly orienta ==Results of a particle extraction==
  7 KB (1,221 words) - 15:46, 24 April 2018
• Seed oversampling
  ...the physical size of the particle and the sidelength that you ask for the particle cropping. ...e with the highest correlation will be kept, and any other particle in the particle radius will be eliminated.
  4 KB (683 words) - 12:51, 3 February 2017
• Shift limits
  ...the ''way'' the limits are imposed (i.e., from which position in the data particle) is controled by <tt> area_search_modus</tt> or <tt>limm</tt>: *2: shifts limits are imposed from the putative position of the particle as computed by a previous iteration.
  1 KB (245 words) - 09:13, 26 October 2016
• Particle File List
  The Particle File List is a [[Generic data containers | generic data container]] that ca ...alue of <tt>tag</tt> property inside the object, '''not''' by the name of particle file (unlike in a classic Dynamo folder).
  7 KB (1,151 words) - 12:01, 30 November 2020
• Subtomogram alignment
  Aligning subtomograms is the process of computing for each available particle the set of shifts and angles that will bring them to a common reference.
  674 bytes (101 words) - 18:02, 29 April 2016
• Daverage
  ...ion (first rotation, then shifting). The shifts and angles that bring the particle to match the template are the ones that parametrize the inverse transform: and the operation that creates the aligned particle can be written as :
  5 KB (792 words) - 14:09, 13 October 2017
• DBox folder
  The ''dBox'' folder is an alternate way to store particle files. When you have, say, 100K files, it is a bad idea to put all of the % file of particle in original folder
  4 KB (570 words) - 14:45, 12 October 2017
• Getting started
  ...': [[Viewing tomograms|viewing]] and [[Catalogue|organizing]] tomograms, [[Particle extraction|extracting particles]], [[Subtomogram alignment|aligning]], aver
  943 bytes (119 words) - 10:08, 26 February 2021
• Cropping table
  A ''cropping table'' is a regular table used in the context of [[particle extraction]]. ''Dynamo'' uses internally tables to execute all particle extraction operations through the [[catalogue]]. If you want to generate [[
  5 KB (787 words) - 13:49, 23 May 2018

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