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• 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
• Table convention
  As a rule, regular users don't necessarily need to remember the structure of a ''Dynamo'' table. However, ...ect, you can set to zero the particles in the [[data folder]] that you don't want to included into the alignment or classification project. Of course, y
  6 KB (809 words) - 09:22, 25 November 2019
• GPUs EMBO 2018
  <tt>dtutorial t -p ptest -M 100 </tt> <br />
  2 KB (365 words) - 12:18, 26 August 2018
• Matlab cell array
  ...a cell array. The same operation may fail on a given model: maybe it doesn't contain enough points, the points are not correctly defined, or any other r
  6 KB (1,039 words) - 17:09, 23 February 2017
• Cross correlation matrix
  They can be used for Hierarchical clustering (using for instance the GUI {{t|dynamo_ccmatrix_analysis}}), but this procedure is normally much weaker tha
  3 KB (471 words) - 12:16, 19 April 2016
• Tarring projects
  ...ther small, probably for demonstration purposes. In real projects, you don't want to transfer around files of several Gb continuously. It is often the
  3 KB (511 words) - 17:47, 6 November 2017
• Montage viewer
  ...>z</tt> levels. Sometimes the default parameters in the montage viewer don't make the scene visible (as the viewing parameters from <tt>dtmslice</tt> ar
  3 KB (414 words) - 14:54, 28 February 2017
• Example of post processing plugin with template update
  Then, you need to pass the syntax of the plugin script. We don't pass the <tt>dynamo_plugin_post</tt> part.
  3 KB (494 words) - 17:36, 3 March 2017
• Customized video montages
  For 1000 elements, you probably don't want to show them all in a single screen, but rather slide through the data ...reuse graphic elements or already available computations, so that they don't need to be recreated each time new frames are generated or recalled.... but
  8 KB (1,261 words) - 10:33, 22 February 2019
• Walkthrough for lattices on vesicles
  When you are finished, don't forget to save the tomogram into the catalogue, using the disk icon (or the ...ed as <tt>tv{i}</tt>, i.e., the entry <tt>i</tt> inside the cell array <tt>t</tt>. We want to generate a single table. Concatenating the table matrixes
  18 KB (3,099 words) - 14:19, 18 August 2021
• Programmatic reconstruction of tomograms
  Stack aligners don't need to be extracted from a <tt>fitter</tt> object. If you computed your al
  3 KB (496 words) - 11:10, 3 July 2018
• Tips for management of tomographic data sets
  Note that the batch numbers don't need to be consecutive. ...e stored as files with name <tt>bXXXtsYYYFull_CatBinned2.mrc</tt>. You don't need to keep track of them. Whenever you select the original full size tomo
  8 KB (1,277 words) - 19:14, 16 May 2017
• Walkthrough on localized reconstruction
  Note that you don't need to be very precise to catch the center of the gold bead. Note that we don't really need to use the object <tt>fgb</tt> as support. Its only role is to
  17 KB (2,770 words) - 11:57, 27 August 2018
• Delft Workshop 2017
  If the [[standalone]] installation works, you don't need to install further elements. However, we advice you to preinstall Matl If it doesn't work, type:
  8 KB (1,246 words) - 13:51, 31 August 2017
• Getting a Structure from Multiple Tomograms of HIV Capsids (walkthrough)
  <tt>dslices(targetFolder,'projy','*','t',finalTable,'align',1,'tag',1:10:500,'labels','on');</tt> <tt>oa = daverage(targetFolder,'t',finalTable,'fc',1);</tt>
  22 KB (3,572 words) - 14:13, 18 August 2021
• Dynamo Workshop CIC bioGUNE 2020
  ...d or not). Please [mailto:daniel.castano@unibas.ch contact us] if you don't get a confirmation on the next days.
  4 KB (570 words) - 18:01, 11 August 2020
• EMBO workshop 2020
  ...e course you need help with Dynamo or subtomogram averaging generally, don't hesitate to ask on the [[https://groups.google.com/forum/#!forum/dynamo-for ...be aware that this setting will only work in Linux and Mac laptops; we don't have an updated ''Dynamo'' version in Windows.
  9 KB (1,391 words) - 16:19, 25 August 2020
• Walkthrough for template matching
  <tt>dgallery -d t20s_Particles.Data -t t20s_Particles.Data/crop.tbl </tt> <tt>oa = daverage('t20s_Particles.Data','t','quickbuffer.tbl'); </tt>
  25 KB (3,943 words) - 14:11, 18 August 2021
• Basel Workshop 2019
  ...ting list. Please [mailto:daniel.castano@unibas.ch contact us] if you don't get a confirmation on the next days.
  4 KB (662 words) - 12:07, 12 October 2021
• Practicals Birkbeck 2019
  <tt>dcm -c fhv -l t</tt> ...necessary: a tomogram with a sidelength on x and y of ~1000 pixels shouldn't pose any visualization problem. Still, in the command line, we can write:
  37 KB (5,792 words) - 20:30, 2 September 2019
• Basel Dynamo Workshop 2018
  ...g list'''. Please [mailto:daniel.castano@unibas.ch contact us] if you don't get a confirmation on the next days.
  5 KB (673 words) - 15:26, 27 August 2018
• Computers Basel 2016
  We are using an old ''Dynamo'' version. Modern ''Dynamo'' versions don't access the MCR library several times.
  5 KB (815 words) - 16:20, 24 August 2017
• Computers Basel 2017
  We are using an old ''Dynamo'' version. Modern ''Dynamo'' versions don't access the MCR library several times.
  5 KB (843 words) - 12:23, 25 August 2017
• File access through predefined profiles
  ...ess them from your Mac system, the catalogue will think that the files don't exist.
  5 KB (870 words) - 16:07, 25 June 2018
• Advanced starters guide (EMBO2021)
  <tt>dcm -c fhv -l t</tt> ...necessary: a tomogram with a sidelength on x and y of ~1000 pixels shouldn't pose any visualization problem. We do it anyway for the exercise with the c
  46 KB (7,267 words) - 12:09, 13 September 2021
• Advanced starters guide
  <tt>dcm -c fhv -l t</tt> ...necessary: a tomogram with a sidelength on x and y of ~1000 pixels shouldn't pose any visualization problem. We do it anyway for the exercise with the c
  47 KB (7,432 words) - 18:41, 3 September 2021
• Dynamo workshop 2017
  ...Please [mailto:daniel.castano@unibas.ch contact us directlyl] if you don't receive a confirmation email in the next couple of days.
  4 KB (649 words) - 10:05, 27 August 2017
• San Diego Workshop 2018
  If the [[standalone]] installation works, you don't need to install further elements in your system. You will be able to follow If it doesn't work, type:
  13 KB (1,774 words) - 19:58, 26 January 2018
• Tilt series alignment workflow folder
  Tilts can be rejected by the alignment algorithm if they don't contain enough markers, or if the error in the markers detected on the tilt
  6 KB (945 words) - 18:06, 6 February 2019
• Integration with Warp and M
  If you collected your data in Tomo rather than SerialEM and don't have mdoc files, you can try [[https://github.com/alisterburt/mdocspoofer m
  6 KB (992 words) - 13:47, 19 August 2020
• Prato Workshop 2019
  Create a Linux term by pressing CTRL+ALT+T.
  6 KB (794 words) - 09:50, 4 April 2019
• Particle File List
  ws = daverage(plf,'t',tMerged); </nowiki>
  7 KB (1,151 words) - 13:01, 30 November 2020
• Postprocessing plugins
  name_projec t= scard.name_project;
  7 KB (1,043 words) - 19:07, 9 March 2017
• Diamond Workshop 2017
  ...ownloading big files from the ''Dynamo'' wiki using <tt>wget</tt>. You don't need to do that, as they have been already downloaded into the location <t
  6 KB (845 words) - 11:55, 7 December 2017
• Dynamo Workshop at the International School of Crystallography 2019
  If it doesn't work, type:
  7 KB (929 words) - 15:17, 5 June 2019
• Pipelines for Workshop Heidelberg 2018
  <tt>o = daverage('oversampling_5.2.Data','t','oversampling_5.2.Data/crop.tbl','fc',1);</tt>
  7 KB (1,014 words) - 10:27, 22 August 2018
• Prebinned tomograms
  ...his option later, by default the tomograms that were already prebinned won't be processed again.
  7 KB (1,183 words) - 16:19, 28 April 2017
• EMBO workshop 2019
  If it doesn't work, type:
  7 KB (944 words) - 11:26, 6 September 2019
• Walkthrough on manual marker clicking
  ...overfitting. Thus, richer parametric models should not be used if you don't have enough markers on each micrograph (in the order of the tens.)
  9 KB (1,526 words) - 20:10, 13 July 2021
• Programmatic control of alignment and reconstruction workflows
  ...es might be excluded during the alignment procedure, even if the user didn't mark them for forceful exclusion. This happens when the gold bead indexing
  12 KB (1,917 words) - 18:35, 10 July 2019
• Walkthrough on PCA through the command line
  <tt>wb = dpkpca.new(name,'t',tableFile,'d',dataFolder,'m',mask);</tt>
  14 KB (1,969 words) - 23:58, 8 February 2021

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