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  • ''Importing models'' refers to the creation of model objects based on coordinates and angles c ...ee that after addition of a model into the tomogram the number of assigned models doesn't change, refresh the GUI pressing the {{t|list volumes}} button.
    3 KB (419 words) - 10:51, 12 March 2020
  • * you want to define precisely and (consequently for all models) the step between two z-levels, or
    5 KB (792 words) - 11:18, 28 February 2017
  • Vesicle models are appropriate when particles are evenly distributed on surfaces reasonabl === From dipole set models ===
    10 KB (1,585 words) - 10:00, 24 February 2017
  • ...vesicle, and using a single <tt>dipole set</tt> model to encompass all the models). Some manipulation [[Vesicle_models#From_dipole_set_models | from the comm
    7 KB (1,266 words) - 17:20, 24 February 2017
  • Linking surfaces with point models is an useful way to get initial orientations of particles. The idea is to a Let's assume you have to models in your workspace: <tt>p</tt> is a general point model, and <tt>s</tt> is a
    2 KB (266 words) - 14:25, 14 July 2017
  • ...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) - 15:52, 12 August 2021
  • ...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) - 09:23, 13 August 2021
  • {{t| myCatalogue/volume_2/models/someModel.omd}} {{t| dwrite(myModel,'myCatalogue/volume_2/models/myModel.omd')}}.
    3 KB (482 words) - 15:54, 23 February 2017

Page text matches

  • ===Adding models from a tomogram===
    626 bytes (93 words) - 13:21, 1 September 2016
  • ...one or models that capture the geometry of the particle distribution. The models will be also kept in the catalogue. ...rite a [[Scripts on sets of models | script]] to visit in one loop all the models and operate on them.
    2 KB (340 words) - 12:31, 23 February 2017
  • The ''model pool'' is the set of models currently hold on MEMORY (and not necessarily on the hard disk). From all the models in the model pool, at any given time only one (or none) is consedered to be
    1 KB (244 words) - 12:27, 22 March 2016
  • === Models ===
    1 KB (226 words) - 09:24, 1 June 2016
  • ''Importing models'' refers to the creation of model objects based on coordinates and angles c ...ee that after addition of a model into the tomogram the number of assigned models doesn't change, refresh the GUI pressing the {{t|list volumes}} button.
    3 KB (419 words) - 10:51, 12 March 2020
  • ...he geometric computations performed on a single model onto a larger set of models. | [[File:modelReuseFilament3Points.png|thumb|upright|400px|three filament models ]]
    4 KB (574 words) - 05:54, 17 August 2016
  • ...include any models visible in the field of view of the rotation frame. The models in the [[model pool]] can be accessed with the same menus also available in [[File:ObliqueViewAuxiliaryModel.png|thumb|center|600px| The models seen in the [[model pool]] of <tt>dtmslice</tt> are also visible here/]]
    3 KB (423 words) - 16:23, 27 April 2017
  • [[Category:Models]] #: Models are naturally integrated inside the [[catalogue]] system, making the proces
    10 KB (1,574 words) - 10:00, 2 May 2017
  • Linking surfaces with point models is an useful way to get initial orientations of particles. The idea is to a Let's assume you have to models in your workspace: <tt>p</tt> is a general point model, and <tt>s</tt> is a
    2 KB (266 words) - 14:25, 14 July 2017
  • ...are used as an easy interface to describe sets of tomograms and attached models. #<nowiki>!</nowiki> Import models from this source
    6 KB (906 words) - 15:24, 10 April 2020
  • {{t| myCatalogue/volume_2/models/someModel.omd}} {{t| dwrite(myModel,'myCatalogue/volume_2/models/myModel.omd')}}.
    3 KB (482 words) - 15:54, 23 February 2017
  • === Loops on models === ...ing [[membrane models]], you frequently use a given series of [[membrane models#Command line| commands]].
    6 KB (1,039 words) - 16:09, 23 February 2017
  • === Command line manipulation of sets of models === ...the approach of saving a ''Model workflow'' and reuse it later on a set of models defined inside the ''Catalogue'' manager <tt>dcm</tt>. This technique may p
    4 KB (698 words) - 09:30, 1 September 2016
  • ...y spherical. If they depart too much from sphericity, you can use membrane models, as done in this walkthrough. == Addition of further models==
    5 KB (872 words) - 22:03, 20 August 2017
  • === Relinking models === ...dcm</tt> with flag <tt> synchronize </tt> tuned to the literal value <tt> models </tt>, i.e.
    5 KB (855 words) - 21:28, 14 August 2017
  • ...allows you to create a catalogue with some small tomograms and predefined models so that you can play with it before using the catalogue on your own data se
    642 bytes (98 words) - 15:10, 27 April 2016
  • ...ogue, and to a particular volume inside the catalogue. This means that the models that are imported, edited and/or saved will be automatically submitted to t ...e as an auxiliary image that is also interactive, allowing the creation of models or the navegation in the tomogram.
    10 KB (1,696 words) - 14:59, 27 November 2020
  • [[Category:Models]] ...d, as membranes or pseudo crystals. The {{t|crop_points}} generated by the models after the geometric computation stage are not supposed to realistically be
    4 KB (683 words) - 12:51, 3 February 2017
  • === From models === Generating tables is the very reason models exist. If you want to generate the table corresponding to a single model {{
    5 KB (787 words) - 13:49, 23 May 2018
  • Vesicle models are appropriate when particles are evenly distributed on surfaces reasonabl === From dipole set models ===
    10 KB (1,585 words) - 10:00, 24 February 2017
  • ...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) - 17:50, 6 February 2020
  • == Models == Models have different plotting methods attached.
    6 KB (1,013 words) - 16:34, 30 October 2017
  • 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) - 15:29, 15 August 2016
  • ...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) - 19:53, 1 February 2017
  • ...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) - 15:46, 24 April 2018
  • === 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) - 10:14, 13 March 2017
  • 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) - 15:07, 25 June 2018
  • == 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) - 19:10, 13 July 2021
  • ...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) - 15:52, 12 August 2021
  • % we create a cell array variable containing all models so that we can loop on it
    3 KB (325 words) - 15:29, 15 August 2016
  • | [[Walkthrough_on_filament_models | Models for filaments]] | [[Walkthrough_on_membrane_models | Models for surfaces]]
    6 KB (894 words) - 17:07, 11 September 2021
  • ...s when you start analysing your data set and you include new tomograms and models on a later stage.
    7 KB (1,151 words) - 12:01, 30 November 2020
  • ...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) - 14:34, 24 January 2022
  • ...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) - 09:23, 13 August 2021
  • ...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) - 15:17, 13 September 2021
  • ...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) - 18:27, 3 September 2021
  • ...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) - 15:19, 28 April 2017
  • ...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) - 13:54, 28 February 2017
  • * Filament models with <tt>dtmslice</tt>
    3 KB (413 words) - 10:12, 19 August 2016
  • * Filament models with <tt>dtmslice</tt>
    3 KB (404 words) - 16:51, 31 August 2016
  • Here <tt>-nc mySurf</tt> will look for models with the string "mySurf" in the name. You should get a reply as: <nowiki>Volume 1. Matching models: 1 (total: 1)
    13 KB (2,062 words) - 11:46, 29 November 2017
  • * Filament models with <tt>dtmslice</tt>
    3 KB (436 words) - 15:09, 9 December 2016
  • * Filament models with <tt>dtmslice</tt>
    4 KB (538 words) - 08:58, 25 August 2017
  • ...as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. 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
    24 KB (3,775 words) - 15:39, 6 September 2021
  • ...arios factors, like "How big is the tomogram?" "Are you going to annotate models on them?". ...annotations produced on different versions of one tomogram. Coordinates of models and particles clicked on binned versions are stored in disk with the correc
    10 KB (1,652 words) - 10:49, 27 June 2018
  • * Filament models with <tt>dtmslice</tt>
    4 KB (604 words) - 21:43, 29 August 2018
  • ...hen considering particles stemming from different tomograms (column 20) or models (column 21).
    5 KB (720 words) - 14:53, 19 May 2016
  • * you want to define precisely and (consequently for all models) the step between two z-levels, or
    5 KB (792 words) - 11:18, 28 February 2017
  • ...defined. How to do that is described in detail in the section ''DipoleSet models'', ''Corrections during picking'' and ''Corrections after picking'' of the ...model for each tomogram. In cases where a different number of tomograms or models is used, the script has to be adapted accordingly.
    22 KB (3,572 words) - 13:13, 18 August 2021
  • * Filament models with <tt>dtmslice</tt>
    5 KB (698 words) - 14:17, 29 August 2019
  • ...6 pixels each. Each volume contains a "model" of a membrane. The different models are coded with the flag <tt>distance</tt>. In this case, the model number
    5 KB (800 words) - 11:09, 9 May 2017
  • === DipoleSet models === Notice that ''Dynamo'' includes several tools for [[vesicle models]], so you might be surprised that for this particular case we go instead fo
    18 KB (3,099 words) - 13:19, 18 August 2021
  • === Creation of models to contain annotations=== ...manually pick some particles. This can be done creating a general or box [[models|model]], which will [[model pool | reside in memory ]] till we save it int
    37 KB (5,792 words) - 19:30, 2 September 2019
  • * Filament models with <tt>dtmslice</tt>
    6 KB (794 words) - 08:50, 4 April 2019
  • ...vesicle, and using a single <tt>dipole set</tt> model to encompass all the models). Some manipulation [[Vesicle_models#From_dipole_set_models | from the comm
    7 KB (1,266 words) - 17:20, 24 February 2017
  • * Filament models with <tt>dtmslice</tt>
    6 KB (845 words) - 10:55, 7 December 2017
  • * Filament models with <tt>dtmslice</tt>
    7 KB (929 words) - 14:17, 5 June 2019
  • * Filament models with <tt>dtmslice</tt>
    7 KB (944 words) - 10:26, 6 September 2019
  • === Creation of models to contain annotations=== ...manually pick some particles. This can be done creating a general or box [[models|model]], which will [[model pool | reside in memory ]] till we save it int
    46 KB (7,267 words) - 11:09, 13 September 2021
  • === Creation of models to contain annotations=== ...manually pick some particles. This can be done creating a general or box [[models|model]], which will [[model pool | reside in memory ]] till we save it int
    47 KB (7,432 words) - 17:41, 3 September 2021
  • * Filament models with <tt>dtmslice</tt>
    7 KB (984 words) - 13:31, 12 April 2018
  • [[File:LocalizedWBPBoxes.png |thumb|center|500px| Boxes-type models are the most suitable for picking in 3D]] ...a 3d coordinate into the model. Further controls are [[dtmslice # editing models | explained here]]
    17 KB (2,770 words) - 10:57, 27 August 2018
  • * Filament models with <tt>dtmslice</tt>
    9 KB (1,391 words) - 15:19, 25 August 2020
  • which asks for a listing of models (<tt>-l m</tt>) in the first volume of the catalogue. Now, we can read both models into memory
    25 KB (3,943 words) - 13:11, 18 August 2021
  • * Filament models with <tt>dtmslice</tt>
    13 KB (1,774 words) - 18:58, 26 January 2018