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• Delft Workshop 2017
  === Tutorial 1: Getting started=== ...kthrough for lattices on vesicles| densely packed spherical geometry ]] (~1 hour)
  8 KB (1,246 words) - 13:51, 31 August 2017
• Walkthrough on adaptive bandpass filtering
  <tt>dtutorial ttest2 -M 50 -noise 0.2 -tight 1 -template ribosome32.em -dshift 0</tt> * <tt>-tight 1</tt> forces the synthetic ribosomes to stay in a box of 32 pixels of sidele
  10 KB (1,461 words) - 20:12, 27 November 2017
• Customized video montages
  <nowiki> for k=1:1000; myData{k} = randn(20000,1);
  8 KB (1,261 words) - 10:33, 22 February 2019
• Walkthrough on command line based tilt series alignment
  u = dtsa(name,'--nogui','-path',folder,'fp',1); </nowiki> ...tilts that are of too bad quality using the following command (e.g., tilt 1 and 40):
  12 KB (1,823 words) - 12:15, 11 August 2021
• Materials Basel 2018
  ...ntification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/ ...ugh for lattices on vesicles| from densely packed spherical geometry ]] (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/
  4 KB (604 words) - 22:43, 29 August 2018
• Walkthrough on PCA through the command line
  <tt>dtutorial ttest128 -M 64 -N 64 -linear_tags 1 -tight 1</tt> for i=1:10
  14 KB (1,969 words) - 23:58, 8 February 2021
• Getting a Structure from Multiple Tomograms of HIV Capsids (walkthrough)
  We prepared a set of 6 tomograms, each containing one Immature HIV-1 virus like particle (VLP) with a layer formed by a lattice of capsid protei ...part of the data that was used in the publication ''An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation'' by Schu
  22 KB (3,572 words) - 14:13, 18 August 2021
• Materials Basel 2019
  ...ntification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/ ...ugh for lattices on vesicles| from densely packed spherical geometry ]] (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/
  5 KB (698 words) - 15:17, 29 August 2019
• Prato Workshop 2018
  <tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt> <tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt>
  7 KB (984 words) - 14:31, 12 April 2018
• Vesicle models
  for i=1:length(ds.dipoles); ...pole set models |dipole set]]) has been defined in the tomogram with index 1 of a catalogue located in the folder <tt>'../catalogues/ctfCorrected</tt> w
  10 KB (1,585 words) - 11:00, 24 February 2017
• Walkthrough on localized reconstruction
  m = dread(oum.files{1}); </nowiki> <nowiki>figure; dslice3d('temp.mrc','r',gb(1,:));</nowiki>
  17 KB (2,770 words) - 11:57, 27 August 2018
• GPU
  ...set}} of 1,2 to. Alternatively, you could run different projects on device 1 and 2. In any case, device 0 is not intended for GPU computing.
  5 KB (902 words) - 08:44, 2 September 2016
• Walkthrough on filament models
  ...ginning of the filament. Note: to correct the anchor point just click the [1] key again.
  6 KB (1,042 words) - 16:52, 12 August 2021
• Walkthrough for lattices on vesicles
  ...mogram is part of the data set used for the paper ''An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation'' by Schu <nowiki>dcmodels hiv -tc dipoleSet -ws o -gm 1
  18 KB (3,099 words) - 14:19, 18 August 2021
• Prato Workshop 2019
  ...sicles| from densely packed spherical geometry on HIV viral capsides]] (~1 hour) ...ntification of proteosomes on a real tomogram through template matching. (~1 hour)
  6 KB (794 words) - 09:50, 4 April 2019
• Cross correlation matrix
  #: p̃_i = F^-1[ F(p_i).* C_ij ]
  3 KB (471 words) - 12:16, 19 April 2016
• Grid hole picker
  * <tt>'runWorkflow'</tt>, with values 0/1. Applies a detection workflow on the polygons. * <tt>'gui' </tt>, with values 0/1. If switched to 0, runs the detection workflow on the polygons without open
  6 KB (1,047 words) - 19:07, 13 February 2017
• Diamond Workshop 2017
  ...sicles| from densely packed spherical geometry on HIV viral capsides]] (~1 hour) ...ntification of proteosomes on a real tomogram through template matching. (~1 hour)
  6 KB (845 words) - 11:55, 7 December 2017
• Dynamo Workshop at the International School of Crystallography 2019
  ...sicles| from densely packed spherical geometry on HIV viral capsides]] (~1 hour) ...ntification of proteosomes on a real tomogram through template matching. (~1 hour)
  7 KB (929 words) - 15:17, 5 June 2019
• Tarring projects
  <pre>dvtar myProject -data 1</pre>
  3 KB (511 words) - 17:47, 6 November 2017
• Workstations EMBO 2016
  <tt>modeltrack.format('force',1);</tt>
  3 KB (499 words) - 20:03, 29 August 2016
• EMBO workshop 2019
  ...sicles| from densely packed spherical geometry on HIV viral capsides]] (~1 hour) ...ntification of proteosomes on a real tomogram through template matching. (~1 hour)
  7 KB (944 words) - 11:26, 6 September 2019
• Walkthrough for template matching
  ...e on a holey carbon grid collected on a Krios + K2. Original pixelsize was 1.76 angstroms. The tomogram provided here has bin binned twice (yielding thu <tt>dynamo_wedge_estimate(fragment,'show',1); </tt>
  25 KB (3,943 words) - 14:11, 18 August 2021
• EMBO workshop 2016
  Thursday, 1 September.
  3 KB (404 words) - 17:51, 31 August 2016
• Utilities for stack creation with the Hagen scheme
  <tt>a.imodAlignFrames('execute',1);</tt>
  3 KB (475 words) - 12:52, 10 March 2017
• Walkthrough model worfklow reuse
  ...n move to a different filament and pick its extremal points with controls [1] and [2]:
  4 KB (574 words) - 06:54, 17 August 2016
• Considerations for tomogram positioning in IMOD
  ...ted offset angle needs to be removed, the following steps need to be done: 1) Go to the "Tomogram Positioning" step and set the "Angle offset" and "Z sh
  4 KB (646 words) - 15:34, 9 April 2019
• Practicals Birkbeck 2019
  <tt>dynamo_catalogue_bin('fhv', 1, 'zchunk', 300); </tt> <tt>dtmslice crop.rec -c fhv -prebinned 1 </tt>
  37 KB (5,792 words) - 20:30, 2 September 2019
• Walkthrough on creation of 3d scenes
  <nowiki>Volume 1. Matching models: 1 (total: 1)
  13 KB (2,062 words) - 12:46, 29 November 2017
• San Diego Workshop 2018
  '''Day 1:''' ...sicles| from densely packed spherical geometry on HIV viral capsides]] (~1 hour)
  13 KB (1,774 words) - 19:58, 26 January 2018
• Multireference alignment
  <tt> dynamo_write_multireference(myTable,'table',myFolder,'refs',1:4,'data',myData,'subset',M/4); </tt>
  4 KB (592 words) - 22:58, 6 June 2018
• Operations on volumes
  ...also pass a mask, so that the normalization will ensure zero mean and std=1 inside the mask.
  4 KB (666 words) - 11:45, 20 April 2017
• Adaptive bandpass filtering
  The alignment of the two half averages proceeds by keeping half average 1 fixed and rotating and shifting half average 2 searching for a cross correl
  4 KB (666 words) - 09:10, 28 November 2017
• Advanced starters guide (EMBO2021)
  <tt>dynamo_catalogue_bin('fhv', 1, 'zchunk', 300); </tt> <tt>dtmslice crop.rec -c fhv -prebinned 1 </tt>
  46 KB (7,267 words) - 12:09, 13 September 2021
• Advanced starters guide
  <tt>dynamo_catalogue_bin('fhv', 1, 'zchunk', 300); </tt> <tt>dtmslice crop.rec -c fhv -prebinned 1 </tt>
  47 KB (7,432 words) - 18:41, 3 September 2021
• Computers Basel 2016
  <pre>tar -xf /Users/gast/workshop2016/dynamo/dynamo_temp_1.1.182.tar -C /Users/gast/workshop2016/dynamo</pre> <pre>!tar -xf /Users/gast/workshop2016/dynamo/dynamo_temp_1.1.182.tar -C /Users/gast/workshop2016/dynamo</pre>
  5 KB (815 words) - 16:20, 24 August 2017
• File access through predefined profiles
  Enabled: 1 ...les through ''repository components'' (documented from release ''Dynamo'' 1.3) has a similar effect, although it is constrained to files that are locat
  5 KB (870 words) - 16:07, 25 June 2018
• Catalogue
  * def=1.2; * ftype =1;
  5 KB (855 words) - 22:28, 14 August 2017
• Starters guide (EMBO2021)
  [[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]] ...0 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search spac
  15 KB (2,422 words) - 16:17, 13 September 2021
• Starters guide (workshop version)
  [[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]] ...0 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search spac
  15 KB (2,427 words) - 19:27, 3 September 2021
• Daverage
  ...ely, one can switch on the flag <tt>implicitRotationMasking</tt> (to value 1). This will compute the values of the rotated volume only inside an interio
  5 KB (792 words) - 15:09, 13 October 2017
• Practical Suggestions for Tomographic Reconstruction
  ...r for the tilt series within this batch. E.g., the tilt series 21 of batch 1 would be named ''b001ts021.st''. The same goes for all other related file t
  5 KB (871 words) - 15:59, 30 April 2019
• Integration with Warp and M
  ...reextract.doc> <table_reextract.tbl> <outputfolder> <sidelength> -asBoxes 1</nowiki>
  6 KB (992 words) - 13:47, 19 August 2020
• EMBO workshop 2021
  <tt> module load dynamo/v1.1.524</tt> ! colspan="4" | '''Day 1'''
  6 KB (894 words) - 18:07, 11 September 2021
• Starters guide
  For ''Dynamo'' version 1.1.115 or higher. <tt>tar -xvf dynamo-v-1.1.50_MCR-8.2.0_GLNXA64.tar </tt>
  24 KB (3,775 words) - 16:39, 6 September 2021
• Construction of masks
  <tt> mask(find(template<threshold))=1; </tt> a{1} = dynamo_sphere(20,128,[64,64,40]);
  6 KB (943 words) - 11:58, 14 September 2017
• Standalone
  <tt>dynamo "for i=1:10;x=rand(64,64,64);dynamo_write(x,sprintf('test%d.em',i));end"</tt>
  7 KB (1,143 words) - 15:56, 4 May 2018
• Walkthrough on membrane models
  ...ne the depiction mesh change the parameter ''subdivision steps'' from 2 to 1. Press the button ''refine the depiction mesh'' once and visualize the resu
  7 KB (1,174 words) - 10:23, 13 August 2021
• Dynamo in Amazon EC2
  ...nstance location should look something like <tt>ec2-52-214-203-126.eu-west-1.compute.amazonaws.com</tt> <tt>Dynamo > dvput pgpu -gpus [0,1] </tt>
  7 KB (1,234 words) - 10:56, 23 October 2017
• Model
  : sets in file array {{t|files}} all model files found inside volume number 1.
  10 KB (1,574 words) - 11:00, 2 May 2017

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