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Anke Mulder, 06/03/2010 12:47 PM
Ace Estimation¶
"ACE: automated CTF estimation." (2005) Mallick SP, Carragher B, Potter CS, Kriegman DJ. Ultramicroscopy. v104(1). PMID: 15935913.
General Workflow:¶
- Make sure that appropriate run names and directory trees are specified. Appion increments names automatically, but users are free to specify proprietary names and directories.
- Select the leginon preset corresponding to the images you'd like to process. Generally "_en" images in leginon are the raw micrographs, but uploaded film data will have a different present. Selecting "all" will simply process all images.
- If tilted data was collected, a dropdown menu provides the option to run CTF correction on selected subsets of tilted or untilted images.
- Make sure that "Commit to Database" box is checked. (For test runs in which you do not wish to store results in the database this box can be unchecked).
- Click on "Run Maxlike Alignment" to submit your job to the cluster. Alternatively, click on "Just Show Command" to obtain a command that can be pasted into a UNIX shell.
- If your job has been submitted to the cluster, a page will appear with a link "Check status of job", which allows tracking of the job via its log-file. This link is also accessible from the "1 running" option under the "Run Alignment" submenu in the appion sidebar.
- Once the job is finished, an additional link entitled "1 ready to upload" will appear under the "Run Alignment" tab in the appion sidebar. Click on this link, and a page will open with a summary of the run output. Clicking on the link next to "reference stack" will open a new window that shows the class averages obtained via this analysis.
- If you are satisfied with the alignment and want to continue processing its output, click on "Upload Job". This shouldn't take too long to finish.
- Now click on the "1 Complete" link under the "Run Alignment" tab. This opens a summary of all alignments that have been done on this project.
- Click on the link next to "reference stack" to open a window that shows the class averages and that contains tools for exploring the result. Such tools include the ability to browse through particles in a given class, create templates for reference based alignment, substack creation,3D reconstruction, etc.
- To perform a feature analysis, click on the grey link entitled "Run Feature Analysis on Align Stack ID xxx".
Notes, Comments, and Suggestions:¶
< CTF Estimation | Create Particle Stack >
Updated by Anke Mulder over 14 years ago · 5 revisions