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• Border alignment artifact
  subplot(1,2,1);dslices(u1);subplot(1,2,2);dslices(u2);
  760 bytes (102 words) - 09:33, 13 October 2017
• Fourier Shell Correlation
  ...is a measure of their similarity. It assigns a coefficient between -1 and 1 to each chosen frequency range. #for each shell index i=1:N/2
  2 KB (357 words) - 08:40, 27 April 2016
• Filament types code example
  points = [1:10:100;1:10:100;1:10:100]'; helixFilament.subunits_dz = 1;
  3 KB (325 words) - 16:29, 15 August 2016
• Example of use of dcoordinates
  v.center = 128.5*[1,1,1]; for i=1:size(t,1);
  2 KB (380 words) - 20:44, 12 February 2019
• Volume center
  ...th the first coordinates in a volume {{t|V}} is thus denoted as {{t|V[1,1,1]}}. ...n of coordinates in a volume is the ''corner'' of the first pixel <tt>[1,1,1]</tt>. This way, the coordinate ''(N,N,N)'' is located exactly in the corne
  6 KB (936 words) - 11:01, 5 March 2018
• Matlab Crash Course 2019
  1. MATLAB Onramp: Interactive course for beginners 1. MATLAB Onramp
  1 KB (173 words) - 11:42, 27 August 2019
• DBox folder
  ...0, the container stores particles whose tags range between 1 and <nn>batch-1<tt>. for i=1:10;
  4 KB (570 words) - 15:45, 12 October 2017
• Example of membrane model workflow through the command line
  view([1,-1,1]); % choses a viewing perspective view([1,-1,1]); box on; axis equal;% again some graphical support
  4 KB (585 words) - 20:53, 1 February 2017
• Shift limits
  *1: shifts limits are imposed from the center of the box <tt> dvput myProject -area_search_modus_r1 1 </tt>
  1 KB (245 words) - 10:13, 26 October 2016
• GPUs EMBO 2018
  <tt>dvput ptest gpu_identifier_set 0:1</tt> <br /> We assign temporarily the gpu identifiers 0 and 1. The queue will assign dynamically some other couple of free identifiers du
  2 KB (365 words) - 12:18, 26 August 2018
• Example of post processing plugin with template update
  % 1: identification of the pipeline stage % 1 from which iteration it is being executed:
  3 KB (494 words) - 17:36, 3 March 2017
• Adding models to catalogued volumes
  ...ode you can define a vesicle model and link it into the volume with index '1' inside the catalogue 'myCatalogue' v.linkCatalogue('myCatalogue','i',1);
  3 KB (482 words) - 16:54, 23 February 2017
• Tomogram-table map file
  <tt>1 /Users/casdanie/test/tomogram_01.mrc </tt> to go along with a table that has only values 1, 2 and 5 in its column 20.
  1 KB (192 words) - 12:23, 26 April 2017
• Walkthrough basic multireference
  <pre >dtutorial ttest -M 8 -N 8 -p pmulti -multi 1 -tight 1 </pre>
  1 KB (221 words) - 13:06, 16 August 2016
• Averaging of subtomograms
  ...each particle will be normalized to have zero mean and standard deviation 1 inside this mask before adding it to the average. <br />- default value is ...[Border alignment artifact | rotation artifacts]] <br />- default value is 1.
  5 KB (818 words) - 18:09, 6 December 2017
• Indicating the missing wedge
  ...m you used, and how it handled the alignment. Lets assume a <tt>ftype</tt> 1 (i.e., column 13 of table will be one). In this geometry, electrons come fr ...le:MissingWedgeminus45To60.png|thumb|upright|400px| missing wedge of type 1 with ''y'' range -45:60]]
  3 KB (548 words) - 12:41, 3 April 2020
• Pasteur workshop 2017
  === Tutorial 1: Getting started===
  2 KB (304 words) - 11:09, 19 July 2017
• GPU identifiers
  <tt>dvput myProject gpus [0,1,2,3]</tt> <tt>export CUDA_VISIBLE_DEVICES="1"</tt>
  1 KB (214 words) - 11:17, 25 October 2017
• Cropping unbinned particles after having worked with binned particles
  Creates the catalogue in full size (let us assume 1 a.u. -arbitrary unit- per pixel) <tt>dynamo_catalogue_bin full_withmodels 1 -ss 256 </tt>
  8 KB (1,292 words) - 18:50, 6 February 2020
• Video tutorials
  ...namo to define local views that are orthogonal to the path between points [1] and [2]. In these local views the user can click on the center of each sec
  1 KB (226 words) - 10:24, 1 June 2016
• Framework for estimation of membrane thickness
  <tt>p = r.getParticle(12,'align',1);</tt> <tt>pa = r.getParticle('*','align',1);</tt>
  5 KB (800 words) - 12:09, 9 May 2017
• Table column convention
  =col 1: tag= 0 or 1
  5 KB (721 words) - 19:41, 8 March 2018
• Volume table index file
  1 myVolume01.mrc
  617 bytes (97 words) - 15:38, 27 April 2016
• Memory/speed balance during ccmatrix computation
  ...''i'' will appear in many independent blocks (in the extremal case ''M''=1, each particle will be read 'N' times), being read from disk and aligned ea
  2 KB (316 words) - 11:14, 19 April 2016
• Walkthrough on command line based tilt series alignment (EMBO2021)
  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):
  6 KB (875 words) - 18:06, 6 September 2021
• Postprocessing plugins
  You need two orders. With the first one you tell ''Dynamo'' that round 1 (for instance) will look for a plugin after normal ''Dynamo'' execution. Fo <tt>dvput ptest plugin_post_r1 1</tt>
  7 KB (1,043 words) - 19:07, 9 March 2017
• Eigencomponents
  ...ntry number 41 is the projection of this particle along eigenvolume number 1, and so on.
  428 bytes (63 words) - 15:50, 26 May 2016
• Multilevel refinement
  <nowiki>cone_range[l] = refine_factor*cone_sampling[l-1]; cone_sampling[l] = cone_sampling[l-1]/2;</nowiki>
  5 KB (786 words) - 10:35, 27 October 2017
• Refined table
  Display the name of the last computed table (by default, from reference 1) <tt>ddb myProjet:t:ite=1 -d</tt>
  2 KB (304 words) - 11:15, 22 April 2016
• Pipelines for Workshop Heidelberg 2018
  The data corresponding to each tilt series is under the folders <tt>work/1</tt> and <tt>work/2</tt>. Intermediate results corresponding to each til <pre>ls work/1
  7 KB (1,014 words) - 10:27, 22 August 2018
• Subboxing
  <tt>locationPenton = r*pentonNormals(1,:);</tt> for position 1 (arbitrarily chosen). Then, the subboxed table can be computed:
  2 KB (374 words) - 17:54, 26 October 2017
• GPUs Basel 2018
  #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1
  4 KB (691 words) - 15:22, 27 August 2018
• Example data sets
  ...[https://drive.google.com/open?id=0B_T9apWxsZjMXzg5SmYxb0JkMUk data set] (~1'3Gb) contains 138 subvolumes, each one with a sidelength of 128 pixels. The
  885 bytes (127 words) - 18:34, 2 May 2016
• Table convention
  1 : tag tag of particle file in data folder 2 : aligned value 1: marks the particle for alignment
  6 KB (809 words) - 09:22, 25 November 2019
• Tilt angle convention
  ...graphs (red) and only right side of micrographs (yellow). If for the tilts 1-20 the left side has a higher defocus, the angles for these tilts should be For visual reference, check Figure 1 in [https://reader.elsevier.com/reader/sd/pii/S1047847717301272?token=8E810
  3 KB (502 words) - 13:42, 10 June 2020
• Matlab cell array
  <tt>disp(a{1});</tt> for i=1:length(myModelFiles)
  6 KB (1,039 words) - 17:09, 23 February 2017
• GPUs EMBO 2016
  : <tt>salloc --gres=gpu:1</tt> : <tt>salloc --gres=gpu:1 --reservation=gpu --time=04:00:00</tt>
  6 KB (1,053 words) - 09:58, 31 August 2016
• Particle File List
  1 <absolute path>/particle_00008.em metadata: [1×1 dpkdata.aux.metadata.StarTable]
  7 KB (1,151 words) - 13:01, 30 November 2020
• GPUs Basel 2019
  #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1
  4 KB (740 words) - 12:51, 27 August 2019
• Oblique slices in tomoslice
  * [Shift] pressed: keeps the frame segment lengths to proportion 1:1
  3 KB (423 words) - 17:23, 27 April 2017
• Particle extraction
  ...]. In general the particles are named with [[Particle|tags]] starting with 1, but some integers might be missing: they correspond to particles that were ...only to the particles actually in the data folder, i.e., the tags (column 1 in table) will only include the ones that correspond to an particle file ac
  7 KB (1,221 words) - 16:46, 24 April 2018
• Considerations for tilt series alignment in IMOD
  ...new alignment and fixing the residuals again it can be lowered further to 1 or even 0.5. ...ment error should preferably be below 2 pixels and in the best cases below 1 pixel. However, this should not be forced. As said before, keep the points
  3 KB (471 words) - 12:57, 27 March 2019
• Volume list file
  #: * ftype = 1 #: * apix = 1.20
  6 KB (906 words) - 16:24, 10 April 2020
• Walkthrough on placement of averages on table positions
  threshold = - 0.1; tSmooth = mbgeom.triangulation.smoothingSubdivision(dt.tr,'mr',1);
  6 KB (925 words) - 11:14, 13 March 2017
• Getting a Structure from Multiple Tomograms of HIV Capsids
  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 protein ...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
  3 KB (489 words) - 15:16, 27 August 2020
• Table
  1 : tag tag of particle file in data folder 2 : aligned value 1: marks the particle for alignment
  8 KB (1,191 words) - 09:50, 1 June 2017
• Filament model
  ...extremal points in the filament, typically in two different sections. <tt>[1]</tt> will appear as a red diamond, <tt>[2]</tt> appears as a blue diamond. | [[File:filamentAnchor1.png|thumb|upright|400px| Click on anchor 1]]
  6 KB (944 words) - 16:29, 15 August 2016
• EMBO workshop 2018
  *Tomogram 1 is called <tt>crop.rec</tt>. The data is a fraction of a tomogram. The ful ...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 Schur
  3 KB (397 words) - 09:01, 5 September 2018
• EMBO workshop 2020
  == Day 1 == <tt>/g/easybuild/x86_64/CentOS/7/haswell/software/Chimera/1.13-foss-2017b-Python-2.7.14/bin/chimera</tt>
  9 KB (1,391 words) - 16:19, 25 August 2020
• Materials Basel 2017
  ...ugh for lattices on vesicles| from densely packed spherical geometry ]] (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/ ...ntification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/
  4 KB (538 words) - 09:58, 25 August 2017
• 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