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• Projects on the command line
  creates an empty project in disk. All the files and folders it points to (masks, data, etc) are just You can also indicate some file parameters while creating the project:
  690 bytes (108 words) - 08:46, 23 May 2016
• Dcp GUI
  ...mo Current Project) is the main tool for interactive design of [[Alignment project| projects]]. ...le and linked to a project, or simply be created during the design of the project using tools indicated by the GUI.
  3 KB (503 words) - 21:57, 13 September 2017
• Project parameter systemNoMPIWrapUnfoldingGPU
  [[Category:project parameters]] [[Category:Advanced project parameters]]
  1 KB (253 words) - 14:57, 22 September 2016
• Adaptive bandpass filtering
  Operationally, an ABP project is just a multireference project that: * and that adjust the lowpass filter parameters at each iteration.
  4 KB (666 words) - 07:10, 28 November 2017
• Angular search
  ...ular grid (i.e., a set of Euler triplets to be scanned) is defined by five parameters: The first four are project parameters that can be chosen by the user and will be applied for the analysis of all
  3 KB (432 words) - 07:56, 2 May 2016
• Alignment project
  [[Category: Alignment Project]] The alignment project is one of the most important objects in Dynamo
  5 KB (793 words) - 07:41, 27 October 2017
• Shift limits
  The shift limiting policy is governed by two parameters: the extent of the allowed limit itself (<tt>area_search</tt> or <tt>lim</t = Changing the shift limits in a project=
  1 KB (245 words) - 08:13, 26 October 2016
• Tarring projects
  Tarring projects is the technique of compacting all information in a project in a single file (called ''tarball''). This file can be then copied to a di * You ran a project in a remote machine where graphical operations are slow, and want to examin
  3 KB (511 words) - 15:47, 6 November 2017
• Refined table
  * columns 4-9 (the alignment parameters) The {{t|ddb}} command provides easy access to the results of the project. Here some examples of syntax
  2 KB (304 words) - 09:15, 22 April 2016
• Multilevel refinement
  ...that produce the maximum correlation in a multilevel fashion. The project parameters <tt>cone_range</tt>, <tt>cone_sampling</tt>, <tt>inplane_range</tt> and <tt In Dynamo, an angular grid is defined by five parameters:
  5 KB (786 words) - 08:35, 27 October 2017
• Averaging of subtomograms
  Averaging of subtomograms means applying an available set of alignment parameters onto a set of data particles and adding them together. Because of the miss ...sion with the <tt>'fweight'</tt>. Note that with the default values of the parameters, this step is ''not'' operated.
  5 KB (818 words) - 16:09, 6 December 2017
• Scripted creation of a project in the Linux command line
  Here we show how to create from scratch a project. This assumes that you already have a [[data folder]], a [[table]],a templ ...for data, etc, which we can use now to show how they can be linked into a project.
  2 KB (400 words) - 09:05, 22 September 2016
• Walkthrough on adaptive bandpass filtering
  == Creating an ABP project with the GUI== ...auxiliary single reference project and then deriving the corresponding ABP project.
  10 KB (1,461 words) - 18:12, 27 November 2017
• MPI Cluster
  ...time you create a project, tell it to use the cluster header to produce a project execution script (extension <tt>.sh</tt>) # Submit the execution script representing the project to your cluster.
  8 KB (1,287 words) - 11:09, 18 September 2017
• Postprocessing plugins
  ...efine an action that ''Dynamo'' will execute after each iteration during a project alignment. * [Medium] Resolution dependent scanning of angular scan parameters.
  7 KB (1,043 words) - 17:07, 9 March 2017
• Multireference alignment
  In a multireference alignment [MRA] project, each particle will be aligned against R different templates. ...an define ''alignment'' masks and ''classification'' masks separately in a project is specially useful when running MRA projects. Very frequently, you want to
  4 KB (592 words) - 20:58, 6 June 2018
• Particle picking
  Sometimes, models carry parameters that need to be tuned for your case (for instance, the radius of [[filament ...[data folder]] that can be used to design an [[alignment project|alignment project]]
  2 KB (340 words) - 11:31, 23 February 2017
• Computers Basel 2017
  # Create alignment project >> computational parameters >> system_gpu # <tt>scp <project.tar> course##@ela.cscs.ch:~/ </tt>
  5 KB (843 words) - 10:23, 25 August 2017
• Alignment mask
  [[Category:alignment project]] In order to to this from <tt>dcp</tt>, you need to go to Numerical Parameters, then switch on the "advanced" button, make sure that the Cross Correlatio
  3 KB (431 words) - 12:29, 15 April 2016
• Hints for improving a refinement
  ...ual resolution and check that your filters ({{t|lowpass}} parameter in the project) are not too coarse in relation to the actual resolution of your average. ...ification mask the ''alignment'' mask that was used by your last alignment project.
  5 KB (720 words) - 13:53, 19 May 2016
• Pipelines for Workshop Heidelberg 2018
  Also, the scripts contain the numerical parameters needed to run the corresponding executable. If you need to edit them, you s The parameters defined in <tt>emboAlignment</tt> concern mainly the size of the gold bead.
  7 KB (1,014 words) - 08:27, 22 August 2018
• Table convention
  ...table. However, it might be useful in order to interprete the results of a project, to check if a table has been correctly generated/imported or to diagnose p ...der]] that you don't want to included into the alignment or classification project. Of course, you can just a table that does not include the particles you wa
  6 KB (809 words) - 07:22, 25 November 2019
• Starters guide (Copenhagen 2024)
  Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen ...e and a table. All of these files we generated before. Start the alignment project GUI by typing
  15 KB (2,427 words) - 12:26, 25 January 2024
• Starters guide (workshop version)
  Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen ...e and a table. All of these files we generated before. Start the alignment project GUI by typing
  15 KB (2,427 words) - 17:27, 3 September 2021
• Starters guide (Göttingen 2024)
  Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen ...e and a table. All of these files we generated before. Start the alignment project GUI by typing
  15 KB (2,427 words) - 11:19, 8 April 2024
• GPU
  ...gned by the system to each device, which you need to enter in a ''Dynamo'' project through the parameter {{t|gpu_identifier_set}} ==Using the GPU in an alignment project==
  5 KB (902 words) - 06:44, 2 September 2016
• Starters guide (EMBO2023)
  Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen ...erated before. You can close all the previous GUIs and start the alignment project GUI by typing
  15 KB (2,422 words) - 14:56, 8 September 2023
• Starters guide (EMBO2021)
  Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen ...erated before. You can close all the previous GUIs and start the alignment project GUI by typing
  15 KB (2,422 words) - 14:17, 13 September 2021
• Starters guide (SciLifeLab 2023)
  Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen ...erated before. You can close all the previous GUIs and start the alignment project GUI by typing
  15 KB (2,424 words) - 14:17, 25 October 2023
• Fourier compensation during averaging
  Then the ''compensated average'' (called simply {{t|average}} inside a project) gets computed by dividing the raw average in fourier space with the comput ...he same particle cropped with a bigger sidelength. During execution of the project, the small particle will be used for alignment (to save time), and the ''co
  4 KB (582 words) - 10:06, 21 November 2017
• Getting help
  ...he list of shipped pdf tutorials and check the syntax of commands, project parameters or database elements.
  2 KB (388 words) - 13:35, 20 May 2016
• Daverage
  ...d line option for averaging particles in a [[data folder]] using alignment parameters expresed inside a [[table]]. ...<tt>i</tt>-th row in a table denote respectively the shifts and rotation parameters that are performed on the template to match the particle in that <tt>i</tt
  5 KB (792 words) - 13:09, 13 October 2017
• Getting a Structure from Multiple Tomograms of HIV Capsids (walkthrough)
  ...ts and their orientations (when visualizing actual results of an alignment project use option '' 'corrected_oriented_positions'' ' instead of the one shown he ...ill use this average as a first reference (template) in the next alignment project. We therefore save the average with
  22 KB (3,572 words) - 12:13, 18 August 2021
• Getting a Structure from Multiple Tomograms of HIV Capsids (Copenhagen 2024)
  ...ts and their orientations (when visualizing actual results of an alignment project use option '' 'corrected_oriented_positions'' ' instead of the one shown he ...ill use this average as a first reference (template) in the next alignment project. We therefore save the average with
  22 KB (3,560 words) - 15:37, 22 January 2024
• Getting a Structure from Multiple Tomograms of HIV Capsids (EMBO2023)
  ...ts and their orientations (when visualizing actual results of an alignment project use option '' 'corrected_oriented_positions'' ' instead of the one shown he ...ill use this average as a first reference (template) in the next alignment project. We therefore save the average with
  22 KB (3,583 words) - 16:27, 8 September 2023
• Particle File List
  This file can be used as input for <tt>average</tt> or an alignment project. You can use a <tt>table</tt> flag in order to pass a table. ...icles, and a table to refer them. This table contains the actual alignment parameters of the particles in the respective data folder.
  7 KB (1,151 words) - 12:30, 6 February 2023
• Principal component analysis
  In whichever way you control the classification project, operatively a PCA based classification will require the completion of thes Additionally, there are some fine tuning parameters that can be passed: particles can be symmetrized, resized or bandpassed.
  3 KB (424 words) - 17:03, 28 March 2020
• EMBO workshop 2020
  ...Projects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...uide | walkthrough]]: creating a catalogue, picking particles, launching a project.
  9 KB (1,391 words) - 14:19, 25 August 2020
• Walkthrough on PCA through the command line (EMBO 2023)
  ...ther 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. == Mathematical parameters ==
  13 KB (1,933 words) - 12:36, 10 September 2023
• Walkthrough on creation of 3d scenes
  ...plate for the full crown. Examples below are given assuming that your best project was named <tt>localized</tt>, substitute if not. Recover the last computed refined table in the data base of your project
  13 KB (2,062 words) - 10:46, 29 November 2017
• Starters guide
  Dynamo is now ready to use. Make a new directory for your project (>> mkdir dtutorial) and go there ...get the list of potential entries for the subject. You can use it without parameters get the list of topics or ask about a particular topic like >> dapropos tab
  24 KB (3,775 words) - 14:39, 6 September 2021
• Walkthrough for lattices on vesicles (EMBO2023)
  == Alignment project == and create a [[alignment project | project]]
  18 KB (3,069 words) - 12:21, 26 October 2023
• Walkthrough for lattices on vesicles
  == Alignment project == and create a [[alignment project | project]]
  18 KB (3,099 words) - 12:19, 18 August 2021
• Walkthrough for lattices on vesicles (Copenhagen 2024)
  == Alignment project == and create a [[alignment project | project]]
  18 KB (3,070 words) - 15:42, 22 January 2024
• Walkthrough on PCA through the command line (SciLifeLab 2023)
  ...ther 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. == Mathematical parameters ==
  13 KB (1,877 words) - 15:17, 26 October 2023
• Walkthrough on PCA through the command line PSI 2023
  ...ther 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. == Mathematical parameters ==
  14 KB (1,967 words) - 17:42, 22 January 2024
• Walkthrough on PCA through the command line
  ...ther 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. == Mathematical parameters ==
  14 KB (1,969 words) - 21:58, 8 February 2021
• Walkthrough on PCA through the command line (Göttingen 2024)
  ...ther 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. == Mathematical parameters ==
  25 KB (3,619 words) - 11:16, 8 April 2024
• Walkthrough on PCA through the command line (Copenhagen 2024)
  ...ther 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. == Mathematical parameters ==
  25 KB (3,619 words) - 08:57, 24 January 2024
• Operations on volumes
  ...e symmetry operators in this command is the one used when defining project parameters.
  4 KB (666 words) - 09:45, 20 April 2017

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