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• Data folder
  ...{{t|myData}}. The name resulting folder {{t|myData}} can then be used as {{t|data folder}} parameter when creating alignment and classification projects ...to keep the same zero padding. You can use fomats {{t|mrc}}, {{t|em}} or {{t|spi}}.
  4 KB (637 words) - 17:48, 30 September 2019
• Seed oversampling
  ...e actual particles will be located, as membranes or pseudo crystals. The {{t|crop_points}} generated by the models after the geometric computation stage The parameter {{t|separation_in_tomogram}} can be tuned (in pixels) at the end of each iterat
  4 KB (683 words) - 13:51, 3 February 2017
• Volume center
  ...rner" with the first coordinates in a volume {{t|V}} is thus denoted as {{t|V[1,1,1]}}. ...e pixel located at <tt> [N/2+1,N/2+1,N/2+1]</tt> as the central pixel of {{t|V}}.
  6 KB (936 words) - 11:01, 5 March 2018
• Library conflicts
  Can't load '<your installation path>/MCRLinux/bin/glnxa64/libmwosgserver.so': dlo Some or all elements in a GUI don't show text characters. In place of text characters, empty square blocks are
  1 KB (218 words) - 16:02, 4 May 2018
• Standalone
  ...ne, it should be tuned to {{t|system_omp}} for multicore projects, or to {{t|system_gpu}} for GPU projects. ...project called {{t|myProject}} will generate an standalone script called {{t|myProject.exe}}. Instead of running the project in the Console shell, the C
  7 KB (1,143 words) - 15:56, 4 May 2018
• Cropping table
  ...e stored in the generated [[data folder]], with names {{t|crop.tbl}} and {{t|}}respectively. ..., and will not be cropped. Thus, it is always useful to use the produced {{t|crop.tbl}} table to initialize an alignment project, as it contains the ide
  5 KB (787 words) - 14:49, 23 May 2018
• Framework for estimation of membrane thickness
  ...particle tag in the data folder will be occupied. For instance, if you don't have a particle labelled wiht 4 in your data folder, you will see it as. <tt> t = dpkfw.mdm.templateSeries('size',[16,16,16],'thickness',1,'distance',[3:7]
  5 KB (800 words) - 12:09, 9 May 2017
• Fourier compensation during averaging
  ...This volume has the size of a particle if Fourier space. It is called an {{t|fweight}} in ''Dynamo''jargon (a Fourier weight) and represents the number ...average in fourier space with the computed fweight. The used function is {{t|dynamo_fweight_divide}}
  4 KB (582 words) - 12:06, 21 November 2017
• Model
  In most models, this stage produces a matrix of points in the field {{t|points}} of the model. ...stage, all models will contain (non empty) fields {{t|crop_points}} and {{t|crop_angles}}. ''Dynamo'' will use them internally if you crop particles wi
  10 KB (1,574 words) - 11:00, 2 May 2017
• Averaging of subtomograms
  ...|metadata]]), use the <tt>[[daverage]]</tt> command, or its GUI version {{t|daverage_GUI}}. {{docfunction|dynamo_average|daverage}}, with the basic syn <tt> o = daverage( data,'t',table); </tt>
  5 KB (818 words) - 18:09, 6 December 2017
• Hints for improving a refinement
  ...you should estimate your actual resolution and check that your filters ({{t|lowpass}} parameter in the project) are not too coarse in relation to the a If inspection of cross correlation and eigencomponents didn't reveal any clear hints of characterizable heterogeneity, you might be stuck
  5 KB (720 words) - 15:53, 19 May 2016
• Getting help
  Even if you don't if the article exists, you can also try your look and launch searches in th will list the main commands attached to the {{t|table}} functionality area.
  2 KB (388 words) - 15:35, 20 May 2016
• Example of membrane model workflow through the command line
  % t = m.grepTable(); % it creates the t variable in the Matlab/Dynamo workspace % dwrite(t,'myTable.tbl'); % writes the matrix into a file
  4 KB (585 words) - 20:53, 1 February 2017
• Projects on the command line
  <tt>dv newProject -d myData -m myMask -t angles.tbl -tm myTemplate.mrc -sm smoothing.mrc -fm fourierMask.mrc -cm cl
  690 bytes (108 words) - 10:46, 23 May 2016
• Programmatic depiction of objects in tomograms
  x = t(:,4)+t(:,24); y = t(:,5)+t(:,25);
  6 KB (1,013 words) - 17:34, 30 October 2017
• Dynamo console
  ...the [[standalone]] can still be used in the console preceding them with {{t|\}}. For instance, all commands inside [[Package notation|packages]] are n To leave a console type {{t|exit}}. Bear in mind that will loose all variables stored in the workspace.
  3 KB (440 words) - 20:59, 12 September 2017
• Particle swapping in multireference projects
  ...different channels can even see different particles, and the channels don't interact with each other.
  1 KB (151 words) - 10:42, 15 April 2016
• Multireference alignment
  ...tead of the name of a file. Same holds for parameters <tt>table</tt> and {{t|fmask}}. You can use different folders for different parameters. ...f valid particles in the table), produce 4 averages, store the files in {{t|myFolder}} and format the individual file names so as to follow the [[#Inpu
  4 KB (592 words) - 22:58, 6 June 2018
• Walkthrough model worfklow reuse
  ...the first we created does contain some crop points, but the other two don't. Then we can pick those filaments that don't contain crop points and select a previously stored workflow to be applied o
  4 KB (574 words) - 06:54, 17 August 2016
• Hints for purchase of computing resources
  For ''Dynamo'' you don't need a lot of memory. If you are planning to buy a machine just for ''Dynam ...wiki/ECC_memory ECC memory check]. However this is a functionality you don't need necessarily need for running subtomogram averaging projects, and purch
  6 KB (966 words) - 15:34, 24 January 2022

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