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  • 591 bytes (90 words) - 12:50, 20 February 2018
  • [[Category:Alignment]] ...nment project]], which will run alignment and averaging in an [[iIterative alignment| iterative way]] in order to gradually improve the attained [[resolution]].
    674 bytes (101 words) - 18:02, 29 April 2016
  • [[Category: alignment]] [[Category: Alignment Project]]
    5 KB (793 words) - 08:41, 27 October 2017
  • [[Category:Multireference Alignment]] In a multireference alignment [MRA] project, each particle will be aligned against R different templates.
    4 KB (592 words) - 21:58, 6 June 2018
  • [[Category:alignment project]] The ''alignment mask'' is use during alignment to define the part of the template cube that will actually be used to align
    3 KB (431 words) - 13:29, 15 April 2016
  • 760 bytes (102 words) - 08:33, 13 October 2017
  • Remember to use the whole path if you are not in the alignment workflow folder. This file is normally generated by ''Dynamo'' when the alignment workflow is created. Note that these angles could also be stored in a diffe
    6 KB (945 words) - 17:06, 6 February 2019
  • Alignment and reconstruction workflows can be used with the GUI or on a totally progr Alignment and reconstruction workflow folders are marked with the extension <tt>.AWF<
    12 KB (1,917 words) - 17:35, 10 July 2019
  • When doing the tilt series alignment in [https://bio3d.colorado.edu/imod/ IMOD], we strongly recommend to consid === Alignment parameters ===
    3 KB (471 words) - 11:57, 27 March 2019
  • ...ased tilt series alignment | walkthrough on command line based tilt series alignment]] shows how to operate this procedure through the command line. = Creating an alignment workflow=
    21 KB (3,161 words) - 23:05, 5 August 2021
  • ...sed mode. The [[Walkthrough on GUI based tilt series alignment | GUI based alignment walkthrough]] shows how to operate this procedure through the GUI. Here, we The following commands create a new alignment workflow in a separate folder. Make sure ''Dynamo'' is running and type the
    12 KB (1,823 words) - 11:15, 11 August 2021
  • ...ased tilt series alignment | walkthrough on command line based tilt series alignment]] shows how to operate this procedure through the command line. = Creating an alignment workflow=
    21 KB (3,158 words) - 16:09, 6 September 2021
  • ...sed mode. The [[Walkthrough on GUI based tilt series alignment | GUI based alignment walkthrough]] shows how to operate this procedure through the GUI. Here, we The following commands create a new alignment workflow in a separate folder. Make sure ''Dynamo'' is loaded and running (
    6 KB (875 words) - 17:06, 6 September 2021

Page text matches

  • [[Category:Alignment]] ...nment project]], which will run alignment and averaging in an [[iIterative alignment| iterative way]] in order to gradually improve the attained [[resolution]].
    674 bytes (101 words) - 18:02, 29 April 2016
  • ...ommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore a good tomogram reconstruction results in perfectly symmetric ...bead. In the Z-view, the beads show symmetric white "wings". Right: A bad alignment causes asymmetries and results in curved or distorted shapes in both views.
    1 KB (221 words) - 15:34, 31 January 2019
  • #REDIRECT [[Multireference alignment]]
    38 bytes (3 words) - 10:29, 22 April 2016
  • [[Category:alignment project]] The ''alignment mask'' is use during alignment to define the part of the template cube that will actually be used to align
    3 KB (431 words) - 13:29, 15 April 2016
  • When doing the tilt series alignment in [https://bio3d.colorado.edu/imod/ IMOD], we strongly recommend to consid === Alignment parameters ===
    3 KB (471 words) - 11:57, 27 March 2019
  • The ''refined table'' is the result of the alignment iteration. ''Dynamo'' produces one refined table per iteration and referenc ...icular, ''Dynamo'' should fill some columns in a ''refined table'' during alignment:
    2 KB (304 words) - 10:15, 22 April 2016
  • [[Category: alignment]] [[Category: Alignment Project]]
    5 KB (793 words) - 08:41, 27 October 2017
  • ...nment parameters, and to locate easily functionalities associated with the alignment of stacks. An important step is to establish the center of the alignment:
    3 KB (496 words) - 10:10, 3 July 2018
  • [[Category:Multireference Alignment]] In a multireference alignment [MRA] project, each particle will be aligned against R different templates.
    4 KB (592 words) - 21:58, 6 June 2018
  • == Oversampling in an alignment project == ...all this procedure ''trimming''). This can be done manually or through the alignment project.
    4 KB (683 words) - 12:51, 3 February 2017
  • ...r one (in order to create a comparison), this average will have a [[border alignment artifact]] resulting from the rotation and shift. If no masking is used, th ...o be aligned to the other, which inevitably creates a sharp edge [[Border alignment artifact| artifact]] in one of the two averages. Applying the same mask on
    1 KB (191 words) - 09:36, 2 May 2016
  • ...ns is heterogeneity. If you are aligning two or more classes together, the alignment would get stuck at some point. If you are lucky, the average will be a sort ...A first approach to diagnose this is to check the cross correlation of the alignment (in column 10 of the [[table]]). A simple inspection of the histogram can
    5 KB (720 words) - 14:53, 19 May 2016
  • ...]] is more time consuming, but it performs simultaneous classification and alignment.
    379 bytes (49 words) - 11:47, 22 March 2016
  • Remember to use the whole path if you are not in the alignment workflow folder. This file is normally generated by ''Dynamo'' when the alignment workflow is created. Note that these angles could also be stored in a diffe
    6 KB (945 words) - 17:06, 6 February 2019
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. === Fiducial based alignment and reconstruction ===
    5 KB (698 words) - 14:17, 29 August 2019
  • Multireference analysis implements simultaneous alignment and classification. ...to have been correctly aligned in the first place. If heterogeneity drives alignment to fail, PCA may not be capable to classify the particles.
    1 KB (215 words) - 09:37, 19 August 2020
  • ...ost widespread ways of simultaneously measuring resolution and driving the alignment is the so called "golden standard" method. A version of this approach is av
    330 bytes (44 words) - 11:39, 14 April 2016
  • ==Introduction: alignment projects== ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
    3 KB (436 words) - 15:09, 9 December 2016
  • ...(for Dynamo Current Project) is the main tool for interactive design of [[Alignment project| projects]]. The GUI follows the pipeline for designing an [[Alignment project]]. To create a new project, just write the name in the <tt>Project<
    3 KB (503 words) - 22:57, 13 September 2017
  • Used when a table is fed into ''Dynamo''as initial table for an alignment project. Value 1 tells ''Dynamo'' that the particle is to be used during an alignment project, values 0 skips the particle.
    5 KB (721 words) - 18:41, 8 March 2018
  • Averaging of subtomograms means applying an available set of alignment parameters onto a set of data particles and adding them together. Because ...particle outside an interior sphere will be discarded to minimize [[Border alignment artifact | rotation artifacts]] <br />- default value is 1.
    5 KB (818 words) - 17:09, 6 December 2017
  • [[Category: Multireference alignment‏‎]] The "golden standard" methodology is a widespread method to drive the alignment process avoiding overfitting and providing an accepted estimation of the at
    4 KB (666 words) - 08:10, 28 November 2017
  • ...sed mode. The [[Walkthrough on GUI based tilt series alignment | GUI based alignment walkthrough]] shows how to operate this procedure through the GUI. Here, we The following commands create a new alignment workflow in a separate folder. Make sure ''Dynamo'' is loaded and running (
    6 KB (875 words) - 17:06, 6 September 2021
  • == Using symmetrization in alignment projects==
    3 KB (429 words) - 14:32, 1 June 2016
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. === Alignment and reconstruction ===
    4 KB (604 words) - 21:43, 29 August 2018
  • ...tomograms through the Dynamo catalogue and to develop good strategies for alignment projects to reach a reasonable structure from a set of tomograms. This is a ...s used in the tutorial (adapted to the different pixelsize) for your first alignment projects.
    3 KB (489 words) - 14:16, 27 August 2020
  • ...a single [[data folder]] that can be used to design an [[alignment project|alignment project]]
    2 KB (340 words) - 12:31, 23 February 2017
  • ...onto the same piece of data. This is an optimal situation for direct space alignment, where the same template is rotated many times and compared to a given part
    715 bytes (111 words) - 12:10, 19 April 2016
  • ...older]], a [[table]],a template, and several masks (for [[Alignment mask|alignment]], classification, description of fourier content of template and [[Smoothi
    2 KB (400 words) - 10:05, 22 September 2016
  • The main idea is to create an alignment project on your local machine, move it to the sciCORE cluster and then run ...ith 128 particles in the directory <code>myParticles</code> and a tutorial alignment project <code>myProject</code>.
    4 KB (740 words) - 11:51, 27 August 2019
  • ...to [[Particle picking|pick particles]] and create [[Subtomogram alignment|alignment]] and [[Classification |classification projects]] to be run on different [
    2 KB (279 words) - 16:40, 6 September 2021
  • ...lder is the minimal input that the [[dcp GUI]] needs in order to create an alignment project. ...{{t|myData}} can then be used as {{t|data folder}} parameter when creating alignment and classification projects,
    4 KB (637 words) - 16:48, 30 September 2019
  • The main idea is that we create an alignment project locally, move it to the cluster on sciCORE and then run it using a ...ith 128 particles in the directory <code>myParticles</code> and a tutorial alignment project <code>myProject</code>.
    4 KB (691 words) - 14:22, 27 August 2018
  • * automated fiducial based tilt-series alignment ...ew [[Walkthrough on command line based tilt series alignment | tilt series alignment tools]]
    6 KB (992 words) - 12:47, 19 August 2020
  • Want to design and alignment problem? Here are some tips:
    885 bytes (127 words) - 17:34, 2 May 2016
  • ==Using the GPU in an alignment project== ...ltireference alignment inherits the "GPU-friendliness" of single reference alignment: the cc of many rotations of the template against the particle can be compu
    5 KB (902 words) - 07:44, 2 September 2016
  • === Tilt series alignment === ...rations_for_tilt_series_alignment_in_IMOD | considerations for tilt series alignment]] with [https://bio3d.colorado.edu/imod/ IMOD].
    5 KB (871 words) - 14:59, 30 April 2019
  • ...g]] tomograms, [[Particle extraction|extracting particles]], [[Subtomogram alignment|aligning]], averaging and [[Classification|classifying]] subtomograms, and
    943 bytes (119 words) - 10:08, 26 February 2021
  • #: alignment parameters A<sub>i</sub> and A<sub>j</sub> ...mal input is a set of particles (formatted as a [[data folder]]) and their alignment parameters (formatted as a [[table]]). You also may want to specify a class
    3 KB (471 words) - 11:16, 19 April 2016
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Some tools for tilt series alignment, reconstruction, CTF correction.
    4 KB (538 words) - 08:58, 25 August 2017
  • * Enhanced tools for manual alignment of tilt series through fiducial markers. * tilt series alignment: improved reload of workflows, allows selection of reconstruction height
    4 KB (558 words) - 10:07, 27 August 2021
  • * Alignment of tilt series with ''Dynamo'' * Independent alignment and resolution determination.
    7 KB (1,014 words) - 09:27, 22 August 2018
  • ...on of tomograms]], and a dedicated computing system (GPUs or clusters) for alignment projects (where the most intensive number crunching occurs) During the alignment stage, [[data folder|cropped particles]] are stored in disk and read into
    2 KB (397 words) - 08:43, 29 April 2016
  • ...sic command line option for averaging particles in a [[data folder]] using alignment parameters expresed inside a [[table]]. Particles and shifted, then rotated, following the alignment parameters in the table. By convention, positions 4:6 and 7:9 in a the <tt
    5 KB (792 words) - 14:09, 13 October 2017
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Manual alignment.
    3 KB (413 words) - 10:12, 19 August 2016
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. * Manual alignment.
    3 KB (404 words) - 16:51, 31 August 2016
  • ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir * Alignment and reconstruction of tilt series.
    4 KB (570 words) - 17:01, 11 August 2020
  • == Alignment ==
    4 KB (698 words) - 09:30, 1 September 2016
  • ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir * Alignment and reconstruction of tilt series.
    4 KB (662 words) - 11:07, 12 October 2021
  • The Fourier Mask that you define on a template during an alignment project describes the Fourier content of the template, ''not'' the one of t
    1 KB (204 words) - 09:25, 6 July 2017
  • ...lization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is requir * Alignment and reconstruction of tilt series.
    5 KB (673 words) - 14:26, 27 August 2018
  • ...ht use this number later for tasks that require parallel processing (e.g., alignment projects): ...to quit ''Dynamo'' every time you want to do something else (e.g., running alignment projects or using chimera). Be aware that if you press ctrl+c within the ''
    6 KB (894 words) - 17:07, 11 September 2021
  • ...ding [[table]] that can be feed into a [[alignment project|project]] for [[alignment]] or [[classification]]. ...ed to define a catalogue. You already have all you need to start designing alignment projects.
    5 KB (855 words) - 21:28, 14 August 2017
  • 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. ...own 8 particles, 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) - 12:01, 30 November 2020
  • === Initial metadata for alignment projects === === Results of alignment iterations ===
    8 KB (1,191 words) - 08:50, 1 June 2017
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...o with Warp and M]] to be able to take advantage of Dynamo for tilt-series alignment and particle picking and plug the results into M's multi-particle refinemen
    9 KB (1,391 words) - 15:19, 25 August 2020
  • While rotating a cube, there is always a [[ Border alignment artifact | rotation artifact]] ...ngth. During execution of the project, the small particle will be used for alignment (to save time), and the ''container'' particles will be used for averaging
    4 KB (582 words) - 11:06, 21 November 2017
  • ...ilt series alignment]] and [[Walkthrough on command line based tilt series alignment ]]. = Fitting to an alignment model =
    9 KB (1,526 words) - 19:10, 13 July 2021
  • Alignment and reconstruction workflows can be used with the GUI or on a totally progr Alignment and reconstruction workflow folders are marked with the extension <tt>.AWF<
    12 KB (1,917 words) - 17:35, 10 July 2019
  • * in alignment projects {{pdftutorial|command_line_projects|link}}
    2 KB (208 words) - 12:19, 29 April 2016
  • ...information on how to do it on each platform) that can be used to run [[alignment project]]s or to initiate an interactive session using the ''Dynamo'' [[Dyn ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
    7 KB (929 words) - 14:17, 5 June 2019
  • ...d by the [[Limiting shifts| shift limiting policy]] used in the particular alignment project. Even though Fourier acceleration is benefitial compared to direct
    2 KB (242 words) - 09:38, 18 April 2016
  • ...information on how to do it on each platform) that can be used to run [[alignment project]]s or to initiate an interactive session using the ''Dynamo'' [[Dyn ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
    7 KB (944 words) - 10:26, 6 September 2019
  • The exception is the Parallel Computing Toolbox: if you want to execute alignment projects inside Matlab using several cores, then you need to buy a license
    1 KB (224 words) - 16:03, 20 April 2017
  • 2 : aligned value 1: marks the particle for alignment ...particles in the [[data folder]] that you don't want to included into the alignment or classification project. Of course, you can just a table that does not in
    6 KB (809 words) - 08:22, 25 November 2019
  • ''Dynamo'' can be run as [[standalone]] on a cluster of CPUs. This works for alignment and classification projects. Using the ''Dynamo'' standalone in a CPU clus ...can however be a problem when you have several thousands particles and the alignment step only covers a few Euler triplets.
    8 KB (1,287 words) - 12:09, 18 September 2017
  • ...sed mode. The [[Walkthrough on GUI based tilt series alignment | GUI based alignment walkthrough]] shows how to operate this procedure through the GUI. Here, we The following commands create a new alignment workflow in a separate folder. Make sure ''Dynamo'' is running and type the
    12 KB (1,823 words) - 11:15, 11 August 2021
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...[[adaptive bandpass filtering]], a way of conducting a ''golden standard'' alignment procedure . (~40 mins)
    6 KB (794 words) - 08:50, 4 April 2019
  • ...://youtu.be/SWKyHrLETPQ youtube link]] shows an introduction to setting up alignment projects in ''Dynamo''. It works on the old {{t|dynamo_project_manager}} GU
    1 KB (226 words) - 09:24, 1 June 2016
  • General operation of the GUI that creates alignment projects. ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
    7 KB (984 words) - 13:31, 12 April 2018
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...[[adaptive bandpass filtering]], a way of conducting a ''golden standard'' alignment procedure . (~40 mins)
    6 KB (845 words) - 10:55, 7 December 2017
  • =Subtomogram alignment and averaging= ...eed an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particl
    15 KB (2,422 words) - 15:17, 13 September 2021
  • =Subtomogram alignment and averaging= ...eed an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particl
    15 KB (2,427 words) - 18:27, 3 September 2021
  • ...is always useful to use the produced {{t|crop.tbl}} table to initialize an alignment project, as it contains the identities of the particles actually on the dat ...6. Including the shifts is crucial if the table expresses the result of an alignment project, as the final ''xyz'' position of the particles will be the additio
    5 KB (787 words) - 13:49, 23 May 2018
  • ...e tomograms through the ''Dynamo'' catalogue and developing strategies for alignment projects to reach a reasonable structure from a set of tomograms. You will ...crop points and their orientations (when visualizing actual results of an alignment project use option '' 'corrected_oriented_positions'' ' instead of the one
    22 KB (3,572 words) - 13:13, 18 August 2021
  • ...ased tilt series alignment | walkthrough on command line based tilt series alignment]] shows how to operate this procedure through the command line. = Creating an alignment workflow=
    21 KB (3,158 words) - 16:09, 6 September 2021
  • ...ased tilt series alignment | walkthrough on command line based tilt series alignment]] shows how to operate this procedure through the command line. = Creating an alignment workflow=
    21 KB (3,161 words) - 23:05, 5 August 2021
  • ...subunits of interest with relation to the center of the average. Then, the alignment [[table]] that produced the average can be used to produce a ''subboxed tab
    2 KB (374 words) - 16:54, 26 October 2017
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
    2 KB (304 words) - 10:09, 19 July 2017
  • ...action that ''Dynamo'' will execute after each iteration during a project alignment.
    7 KB (1,043 words) - 18:07, 9 March 2017
  • ...icles. Thus, you need a [[data folder]] and a [[table]] that describes the alignment.
    3 KB (424 words) - 18:03, 28 March 2020
  • :-Alignment of axes in orthogonal orientations
    3 KB (423 words) - 16:23, 27 April 2017
  • ...aging, some steps in [[PCA]] analysis, manual management of models. Even [[alignment project]]s with modest number of particles can be reasonably executed on a ...tion, cropping particles, and any preprocessing related to the creation of alignment project. Once the project has been created (as a folder and an execution sc
    6 KB (948 words) - 13:27, 8 May 2017
  • Masks are initiated to default values. This means spherical masks for alignment and classification masks, and full cubes for smoothing and fourier mask of Then select the number of available cores for alignment and averaging.
    10 KB (1,461 words) - 19:12, 27 November 2017
  • ...describes the basics including particle picking, initial model generation, alignment, averaging and classification or particles. ''Dynamo'' has a standalone to ...:StartersGuideParticlesUnaligned.png|thumb|center|400px| Particles without alignment (<tt>table</tt> is switched off).]]
    24 KB (3,775 words) - 15:39, 6 September 2021
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
    3 KB (397 words) - 08:01, 5 September 2018
  • ...rder to make easy to keep track on the processing steps already performed (alignment, reconstruction), the location of the intermediate results, and their bindi In this example, we assume that you are using <tt>imod</tt> for tomographic alignment and reconstruction of each tilt series. The raw data is stored in a tree be
    8 KB (1,277 words) - 18:14, 16 May 2017
  • ...to ease computations, a binning order is passed to the [[Alignment project|alignment]] or classification project.
    8 KB (1,292 words) - 17:50, 6 February 2020
  • ...will depend on the reconstruction program you used, and how it handled the alignment. Lets assume a <tt>ftype</tt> 1 (i.e., column 13 of table will be one). In
    3 KB (548 words) - 11:41, 3 April 2020
  • This shell is "activated" and can then be used to run [[alignment project]]s or to initiate an interactive session using the ''Dynamo'' [[Dyn
    3 KB (551 words) - 14:01, 22 June 2018
  • ...step and set the "Angle offset" and "Z shift" to zero. 2) Go to the "Fine Alignment" step and set the two values to zero too. Do ''not'' go back to the "Tomogr
    4 KB (646 words) - 14:34, 9 April 2019
  • ...n be used directly by ''Dynamo'' to operate an extraction and a subsequent alignment. ...s that are poorly defined still have a chance to get driven by a posterior alignment to the center of the box. If we initialize some variables:
    18 KB (3,099 words) - 13:19, 18 August 2021
  • ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...[[adaptive bandpass filtering]], a way of conducting a ''golden standard'' alignment procedure . (~40 mins)
    13 KB (1,774 words) - 18:58, 26 January 2018
  • ...than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a table that expreses the alignment
    14 KB (1,969 words) - 22:58, 8 February 2021
  • === Through manual alignment === ====Manual alignment of some particles ====
    25 KB (3,943 words) - 13:11, 18 August 2021
  • ...b>sc</sub>'' and determined by the rotation axis implicitly defined by the alignment. Now, we could find the actual positions of the gold beads with an alignment project. We create a spherical template and mask:
    17 KB (2,770 words) - 10:57, 27 August 2018
  • #run your alignment by typing <tt>srun my_project.exe</tt>
    5 KB (815 words) - 15:20, 24 August 2017
  • # Create alignment project >> computational parameters >> system_gpu
    5 KB (843 words) - 11:23, 25 August 2017
  • [ 2 ] marked for alignment: 22 == Project for rotational alignment ==
    37 KB (5,792 words) - 19:30, 2 September 2019
  • This framework is more useful in plastic sections. The premise is that an [[alignment project]] has been created to fix the position an orientation of a set of p
    5 KB (800 words) - 11:09, 9 May 2017

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