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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 align3 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 diffe6 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 the12 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
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- [[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 align3 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 on1 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 can5 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 diffe6 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 av330 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
