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• Operations on tables
  ...function|dynamo_table_grep|dtgrep}}. Commands are {{t|<}}, {{t|top}} and {{t|bottom}. In order to create a subtable with a predefined set of tags, use the flag{{t|tags}}:
  2 KB (300 words) - 11:35, 23 May 2016
• Dcm
  The command {{t|dcm}} extends the functionalities of the [[dcm GUI]] for creating and manag While the GUI offers quick tools for visiting the tomograms, the {{t|dcm}} command is normally more comfortable for global operations or data ex
  626 bytes (93 words) - 14:21, 1 September 2016
• Volume table index file
  ...ex file is a text file stored inside a [[data folder]], and has the name {{t|indices_column20.doc}}. An example structure could be: ...able| table] {{t|crop.tbl}} in the same data folder. Note that numbers don't need to correlate.
  617 bytes (97 words) - 15:38, 27 April 2016
• Video tutorials
  ...tion to setting up alignment projects in ''Dynamo''. It works on the old {{t|dynamo_project_manager}} GUI. In this [https://youtu.be/VPIdxpxNqWw video] we use {{t|dtmview}} to show how the concurrent viewers can be used to pick isolated p
  1 KB (226 words) - 10:24, 1 June 2016
• Importing models
  ...e number of assigned models doesn't change, refresh the GUI pressing the {{t|list volumes}} button. === Import with {{t|dmiport}} ===
  3 KB (419 words) - 11:51, 12 March 2020
• Refined table
  The {{t|ddb}} command provides easy access to the results of the project. Here some <tt>ddb myProjet:t -d</tt>
  2 KB (304 words) - 11:15, 22 April 2016
• Adding models to catalogued volumes
  ...|tomogram viewers]] for the volume indexed as 2 in a [[catalogue]] named {{t|myCatalogue}} will be automatically stored in the position: {{t| myCatalogue/volume_2/models/someModel.omd}}
  3 KB (482 words) - 16:54, 23 February 2017
• Binning tomograms
  reads the file {{t|myVolume.mrc}} into the variable {{t|a}}. For a volume {{t|4k x 4k x 400}}, it takes 6 minutes on a MacBookPro (i5), during which the ...l probably use less than one second, as {{t|b}} is 64 times smaller than {{t|a}}.
  3 KB (453 words) - 10:49, 20 May 2016
• GPU identifiers
  ...rectly ssh onto the node where the GPUs are installed) can be shown with {{t|nvidia-smi}}. The system assigns an integer number to each device CUDA can ...identifier_set}} (short {{t|gpus}}). You can set it into a project using {{t|dvput}}, for instance:
  1 KB (214 words) - 11:17, 25 October 2017
• Dynamo catalogue tutorial
  The {{t|dctutorial}} (''Dynamo'' catalogue tutorial) allows you to create a catalog Other tools for creation of phantom catalogues can be found directy in the {{t|Help}} menu of the [[dcm GUI]].
  642 bytes (98 words) - 16:10, 27 April 2016
• Operations on volumes
  ...contents of the file {{t|myFile.mrc}} and write the result into the file {{t|binned.mrc}} ...s accept as input indistinctly a filename or a variable. Note also that {{t|dread}} accepts the alternative command line syntax:
  4 KB (666 words) - 11:45, 20 April 2017
• GPU
  After untarring the tar package in location {{t|DYNAMO_ROOT}}, go to ...hat you have CUDA active in your shell, for instance look for the NVIDIA {{t|nvcc}} compiler:
  5 KB (902 words) - 08:44, 2 September 2016
• Example of use of dcoordinates
  t = v.grepTable(); for i=1:size(t,1);
  2 KB (380 words) - 20:44, 12 February 2019
• Adaptive bandpass filtering
  * doesn't [[Particle swapping in multireference projects | swap particles]] between r ...etting ''Dynamo'' derive an ABP project, which will be generally called {{t|myProject_eo}}. An example can be followed in [[Walkthrough on adaptive ban
  4 KB (666 words) - 09:10, 28 November 2017
• Memory/speed balance during ccmatrix computation
  ...ill be read 'N' times), being read from disk and aligned each time. We don't want this. But in the other hand, if ''M'' is too big (in the extreme case, ...ynamo_ccmatrix_project_manager}} to get some hints about how to tune the {{t|batch}} parameter, which corresponds to ''M''. Basically the user is inform
  2 KB (316 words) - 11:14, 19 April 2016
• Construction of masks
  ...ith several geometrical options: spheres, ellipsoids, tubes, cylinders. {{t|dmask}} can be used from the command line. ...are other commands for specific geometries: {{t|dsphere}}, {{t|dshell}}, {{t|dcylinder}}....
  6 KB (943 words) - 11:58, 14 September 2017
• Helical symmetry
  Symmetrizing a helical particle can be done with the usual tool {{t|dsym}}: where {{t|operator}} represents any symmetry operator. The syntax for helical operato
  3 KB (429 words) - 15:32, 1 June 2016
• Volume list file
  Volume list files are text files with extension {{t|.vll}}. They are used as an easy interface to describe sets of tomograms a ...d with the symbol <nowiki>></nowiki>. For instance, if we write the file {{t|example.vll}} as
  6 KB (906 words) - 16:24, 10 April 2020
• MPI Cluster
  ...ling ''Dynamo'' on your cluster requires an additional step involving a {{t|cc}} compiler available on your side that links the MPI libraries. In most ...add some compilers to your path. They are typically called {{t|mpiCC}}, {{t|mpicc}}... It is a good idea to check the availability and syntax of the co
  8 KB (1,287 words) - 13:09, 18 September 2017
• Spectral averages in PCA
  Whenever you use the {{t|dynamo_ccmatrix_analysis}} GUI to run a [[subaverage]], the results are as The database item {{t| subaverage}} needs an additional locator for the experiment number.
  2 KB (351 words) - 15:53, 26 May 2016

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