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  • 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<sub>i</sub> = F<sup>-1</sup>[ F(p<sub>i</sub>).* C<sub>ij</sub> ]
    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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