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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
• 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
• 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

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