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• Cropping unbinned particles after having worked with binned particles
  ...t, comprising 3 full sized tomograms, each one containing already a model. Models are simple clouds of points. Now we import the models residing in the "unbinned catalogue''. Note that in "real life" you do not
  8 KB (1,292 words) - 18:50, 6 February 2020
• Programmatic depiction of objects in tomograms
  == Models == Models have different plotting methods attached.
  6 KB (1,013 words) - 17:34, 30 October 2017
• Filament model
  Filament models are used for geometries where location and orientation of particles to be c ...ns along the path of the filament and picking the central point. Different models are available for the different relationships between the "backbone" of the
  6 KB (944 words) - 16:29, 15 August 2016
• Example of membrane model workflow through the command line
  ...the operations typically operated by the cropping workflow of a [[membrane models|membrane model]]. ...g of membrane modes) are the ones listed in the description of [[Membrane models#Command line | command line methods attached to this model]]. <br>
  4 KB (585 words) - 20:53, 1 February 2017
• Particle extraction
  ...es''. A new GUI will popup, with a list of models. You can then select the models that already contain ''crop points''). Then click on ''Create list''. This ...opping information in a text file: a list of tomogram files, and a list of models or tables to be used on each tomogram. For instance:
  7 KB (1,221 words) - 16:46, 24 April 2018
• Walkthrough on placement of averages on table positions
  === As several volume models === ...e previous one, we are using the same starting isolevel for the individual models, and also we are passing the order to Chimera to open the surface that we c
  6 KB (925 words) - 11:14, 13 March 2017
• File access through predefined profiles
  A frequently happening example are the tomograms and models in the [[catalogue]]. If you produced your catalogue in the linux machine, ...the calatogue gui to "relink" the tomograms (and linking elements in the models) to the mac convention. This works, but is rather tedious. Moreover, it als
  5 KB (870 words) - 16:07, 25 June 2018
• Walkthrough on manual marker clicking
  == Extended fitting models == ...wer error value, this might be due to overfitting. Thus, richer parametric models should not be used if you don't have enough markers on each micrograph (in
  9 KB (1,526 words) - 20:10, 13 July 2021
• Walkthrough on filament models
  ...t subtomograms from filament-like structures using the ''Dynamo'' filament models. ...tomogram entry appears in the catalogue manager. Any further annotations (models) to the tomogram will be linked to this entry. Select the entry and open it
  6 KB (1,042 words) - 16:52, 12 August 2021
• Filament types code example
  % we create a cell array variable containing all models so that we can loop on it
  3 KB (325 words) - 16:29, 15 August 2016
• EMBO workshop 2021
  | [[Walkthrough_on_filament_models | Models for filaments]] | [[Walkthrough_on_membrane_models | Models for surfaces]]
  6 KB (894 words) - 18:07, 11 September 2021
• Particle File List
  ...s when you start analysing your data set and you include new tomograms and models on a later stage.
  7 KB (1,151 words) - 13:01, 30 November 2020
• Hints for purchase of computing resources
  ...cropping, averaging, some steps in [[PCA]] analysis, manual management of models. Even [[alignment project]]s with modest number of particles can be reasona ...eed for running subtomogram averaging projects, and purchase more economic models like the ones described above is deemed safe.
  6 KB (966 words) - 15:34, 24 January 2022
• Walkthrough on membrane models
  ...uctures with large surfaces (e.g., membranes) using the ''Dynamo'' surface models. ...tomogram entry appears in the catalogue manager. Any further annotations (models) to the tomogram will be linked to this entry. Select the entry and open it
  7 KB (1,174 words) - 10:23, 13 August 2021
• Starters guide (EMBO2021)
  ...as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the to Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (c
  15 KB (2,422 words) - 16:17, 13 September 2021
• Starters guide (workshop version)
  ...as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the to Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (c
  15 KB (2,427 words) - 19:27, 3 September 2021
• Prebinned tomograms
  ...to declare in which catalogue we are opening the tomogram, i.e., where the models that we create during this session will be created. When you open a file by invoking one prebinned version, the models will be annotated with the right size (i.e., in voxel coordinates of the or
  7 KB (1,183 words) - 16:19, 28 April 2017
• Montage viewer
  ...sual application of the montage viewer is for the annotation of [[membrane models]], as explained with detail in the [[Montage viewer for membrane picking |w
  3 KB (414 words) - 14:54, 28 February 2017
• Materials Basel 2016
  * Filament models with <tt>dtmslice</tt>
  3 KB (413 words) - 11:12, 19 August 2016
• EMBO workshop 2016
  * Filament models with <tt>dtmslice</tt>
  3 KB (404 words) - 17:51, 31 August 2016

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