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- ...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) - 17:09, 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 running and type the12 KB (1,823 words) - 12:15, 11 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 loaded and running (6 KB (875 words) - 18:06, 6 September 2021
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- ...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) - 10:36, 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) - 15:53, 19 May 2016
- ...]] is more time consuming, but it performs simultaneous classification and alignment.379 bytes (49 words) - 12:47, 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) - 18:06, 6 February 2019
- ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. === Fiducial based alignment and reconstruction ===5 KB (698 words) - 15:17, 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) - 10:37, 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) - 12:39, 14 April 2016
- ==Introduction: alignment projects== ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.3 KB (436 words) - 16:09, 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) - 23:57, 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) - 19:41, 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) - 18:09, 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 at4 KB (666 words) - 09:10, 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) - 18:06, 6 September 2021
- == Using symmetrization in alignment projects==3 KB (429 words) - 15:32, 1 June 2016
- ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. === Alignment and reconstruction ===4 KB (604 words) - 22:43, 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) - 15:16, 27 August 2020
- ...a single [[data folder]] that can be used to design an [[alignment project|alignment project]]2 KB (340 words) - 13:31, 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 part715 bytes (111 words) - 13:10, 19 April 2016
- ...older]], a [[table]],a template, and several masks (for [[Alignment mask|alignment]], classification, description of fourier content of template and [[Smoothi2 KB (400 words) - 11:05, 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) - 12:51, 27 August 2019
