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• Catalogue
  ...ograms and you don't want to extract the tomograms again, you probably don't need to define a catalogue. You already have all you need to start designin ...ed by the catalogue are expressed through their ''absolute path'', you don't need to do anything especial.
  5 KB (855 words) - 22:28, 14 August 2017
• Installation
  ...ds|download]], choose a location in your file system, which we will call {{t|DYNAMO_ROOT}} in this page. If you use your own MCR libraries, you should also make certain that the {{t|$LD_LIBRARY_PATH}} environment variable is correctly set to include all the
  3 KB (551 words) - 15:01, 22 June 2018
• Daverage
  <tt> output = daverage('myData','t','myTable.tbl');</tt> <tt> daverage myData -t myTable.tbl -ws output</tt>
  5 KB (792 words) - 15:09, 13 October 2017
• DBox folder
  ''Dynamo'' uses a class called {{t|dBoxes}} to manage this kind of [[Generic data containers|generic data cont o = daverage('data.Boxes','t',globalTable);
  4 KB (570 words) - 15:45, 12 October 2017
• Dynamo Matlab version
  If your institution doesn't provide you with Matlab licenses, ''Dynamo'' can be fully run using its [[s
  1 KB (224 words) - 17:03, 20 April 2017
• Viewing tomograms
  ...ide dtmslice and automatically assign it to a {{t|default}} catalogue. Don't do this if you are not certain that the full tomogram will fit in memory. I Sliding montages are normally invoked through the {{t|Montage}} tab of {{t|dtmslice}}.
  10 KB (1,652 words) - 11:49, 27 June 2018
• GPUs EMBO 2016
  We call this the ''console shell''. In this console shell, we don't have don't need to have access to a GPU. We are using an old ''Dynamo'' version. Modern ''Dynamo'' versions don't access the MCR library several times.
  6 KB (1,053 words) - 09:58, 31 August 2016
• Project parameter systemNoMPIWrapUnfoldingGPU
  In this case, you don't really need an MPI system (as you'll only take to one node), but you still
  1 KB (253 words) - 16:57, 22 September 2016
• Walkthrough on adaptive bandpass filtering
  Table, template and masks don't need special formatting. We will just provide ''Dynamo'' with the default o * We don't let the parameters drive away from the center of the particle (limit modus
  10 KB (1,461 words) - 20:12, 27 November 2017
• Membrane models
  ...z-planes and introduce membrane points by clicking on them. The slices don't need to be accessed in any order. However, the set of points clciked in a g This procedure works well when you don't need a lot precision when moving to a ''z'' plane to the next one.
  5 KB (792 words) - 12:18, 28 February 2017
• Workshop exercises
  You want to reproduce the data folder with bigger particles, but don't remember how you used the Catalogue to generate the data folder (maybe some ...m and a text file with 3D coordinates. It's a simple situation, so you don't want to use the ''Catalogue'' to crop particles from the tomogram in the po
  4 KB (698 words) - 10:30, 1 September 2016
• Particle extraction
  ...d data folder. This table is stored inside the data folder with the name {{t|crop.tbl}}. ...omogram number'' used in the column 20 of the [[#Table|produced table]] {{t|crop.tbl}}. This file, jointly with the table, makes possible to track from
  7 KB (1,221 words) - 16:46, 24 April 2018
• Cropping unbinned particles after having worked with binned particles
  <tt>dcm -c full_withmodels -l t -ws o</tt> <tt>ddbrowse -d targetData -t targetData/crop.tbl </tt>
  8 KB (1,292 words) - 18:50, 6 February 2020
• Euler angles convention
  # tdrot (for '''t'''ilt '''d'''irection gets '''rot'''ated)
  2 KB (320 words) - 23:26, 4 August 2016
• Vesicle models
  ...ogram density map in a later stage. If such a fitting is possible, you don't need to spend too much time trying to make your manual picking too precise, ...This is useful when you have several vesicles in one tomogram, and you don't want to initiate a vesicle model for each one of them. The [[dipole set mod
  10 KB (1,585 words) - 11:00, 24 February 2017
• Table column convention
  {{T|hola}} ...d from the average for different reasons, mainly because its cc score didn't qualify it to pass the threshold selected by the user.
  5 KB (721 words) - 19:41, 8 March 2018
• Dtmslice
  ...s in the scene with the box tool in the toolbar or simply by clicking on {{t|[v]}}. The boxes in the scene define regions that can be used for different ...d, you can plot on it with any regular command. For instance, the Matlab {{t|plot3}} command:
  10 KB (1,696 words) - 15:59, 27 November 2020
• MCR libraries
  ...ion available for [[Download Dynamo|download]] and in general you shouldn't need to reinstall them.
  2 KB (369 words) - 11:33, 4 October 2016
• Walkthrough on creation of 3d scenes
  <tt>ddb localized:rt -r t</tt> <tt>dwrite(t,'alignmentLocalRefinement.tbl');</tt>
  13 KB (2,062 words) - 12:46, 29 November 2017
• Scripted creation of a project in the Linux command line
  ...template and [[Smoothing mask|smoothing while FSC computing]]). If you don't you can just run (in the linux shell) the command:
  2 KB (400 words) - 11:05, 22 September 2016

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