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• Hints for improving a refinement
  ...ual resolution and check that your filters ({{t|lowpass}} parameter in the project) are not too coarse in relation to the actual resolution of your average. ...ification mask the ''alignment'' mask that was used by your last alignment project.
  5 KB (720 words) - 15:53, 19 May 2016
• Table convention
  ...table. However, it might be useful in order to interprete the results of a project, to check if a table has been correctly generated/imported or to diagnose p ...der]] that you don't want to included into the alignment or classification project. Of course, you can just a table that does not include the particles you wa
  6 KB (809 words) - 09:22, 25 November 2019
• Starters guide (workshop version)
  Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen ...e and a table. All of these files we generated before. Start the alignment project GUI by typing
  15 KB (2,427 words) - 19:27, 3 September 2021
• Starters guide (EMBO2021)
  Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen ...erated before. You can close all the previous GUIs and start the alignment project GUI by typing
  15 KB (2,422 words) - 16:17, 13 September 2021
• GPU
  ...gned by the system to each device, which you need to enter in a ''Dynamo'' project through the parameter {{t|gpu_identifier_set}} ==Using the GPU in an alignment project==
  5 KB (902 words) - 08:44, 2 September 2016
• Fourier compensation during averaging
  Then the ''compensated average'' (called simply {{t|average}} inside a project) gets computed by dividing the raw average in fourier space with the comput ...he same particle cropped with a bigger sidelength. During execution of the project, the small particle will be used for alignment (to save time), and the ''co
  4 KB (582 words) - 12:06, 21 November 2017
• Daverage
  ...d line option for averaging particles in a [[data folder]] using alignment parameters expresed inside a [[table]]. ...<tt>i</tt>-th row in a table denote respectively the shifts and rotation parameters that are performed on the template to match the particle in that <tt>i</tt
  5 KB (792 words) - 15:09, 13 October 2017
• Getting help
  ...he list of shipped pdf tutorials and check the syntax of commands, project parameters or database elements.
  2 KB (388 words) - 15:35, 20 May 2016
• Getting a Structure from Multiple Tomograms of HIV Capsids (walkthrough)
  ...ts and their orientations (when visualizing actual results of an alignment project use option '' 'corrected_oriented_positions'' ' instead of the one shown he ...ill use this average as a first reference (template) in the next alignment project. We therefore save the average with
  22 KB (3,572 words) - 14:13, 18 August 2021
• 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. ...icles, 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
• Principal component analysis
  In whichever way you control the classification project, operatively a PCA based classification will require the completion of thes Additionally, there are some fine tuning parameters that can be passed: particles can be symmetrized, resized or bandpassed.
  3 KB (424 words) - 19:03, 28 March 2020
• EMBO workshop 2020
  ...Projects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...uide | walkthrough]]: creating a catalogue, picking particles, launching a project.
  9 KB (1,391 words) - 16:19, 25 August 2020
• Walkthrough on creation of 3d scenes
  ...plate for the full crown. Examples below are given assuming that your best project was named <tt>localized</tt>, substitute if not. Recover the last computed refined table in the data base of your project
  13 KB (2,062 words) - 12:46, 29 November 2017
• Starters guide
  Dynamo is now ready to use. Make a new directory for your project (>> mkdir dtutorial) and go there ...get the list of potential entries for the subject. You can use it without parameters get the list of topics or ask about a particular topic like >> dapropos tab
  24 KB (3,775 words) - 16:39, 6 September 2021
• Walkthrough on PCA through the command line
  ...ther 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. == Mathematical parameters ==
  14 KB (1,969 words) - 23:58, 8 February 2021
• Walkthrough for lattices on vesicles
  == Alignment project == and create a [[alignment project | project]]
  18 KB (3,099 words) - 14:19, 18 August 2021
• Operations on volumes
  ...e symmetry operators in this command is the one used when defining project parameters.
  4 KB (666 words) - 11:45, 20 April 2017
• Tips for management of tomographic data sets
  The contents of the <tt>raw</tt> folder may vary from project to project. They might be unaligned movies, gain reference files, or any intermediate ...r opening the live gallery you are most likely to need to adjust depiction parameters as binning level, bandpass or number of projected slices per tomogram.
  8 KB (1,277 words) - 19:14, 16 May 2017
• Practicals Birkbeck 2019
  ...ed in the slice... in such a case, you probably want to check the tracking parameters before using <tt>o</tt> again! == Project for rotational alignment ==
  37 KB (5,792 words) - 20:30, 2 September 2019
• Advanced starters guide (EMBO2021)
  == Project to find membrane orientations== We can create a project directly thorugh the command line:
  46 KB (7,267 words) - 12:09, 13 September 2021

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