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• 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

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