More Stack Tools¶

This is an overview of the different tools available for manipulating stacks in appion.

General Workflow:¶

1. 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.
2. Select the particle selection run to use for boxing from the drop down menu.
3. Enter a run description.
4. Enter a box size
5. Select the appropriate preset of images to search (default is en if you collected with leginon).
6. From the drop down menu, select whether you want to box particles on tilted images as well (for RCT and OTR, make two separate stacks for tilted and untilted particles!)
7. Check these boxes if you are creating this stack concurrent with data collection, particle selection, and CTF estimation. Appion will wait for more picms to roll in.
8. You can pre-filter particles in accordance with your rejection (hide) or exemplar decisions in the image viewer and/or using the image assessment tool.
9. 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).
10. Check the "invert image density" box if you collected ice data and wish to perform 2D alignment and classification. Also, if you wish to normalize your stack to STDEV of 1.0, select the "Normalize Stack Particles" box.
11. To apply CTF correctio, select the "Ctf Correct Particle Images" box, and choose the CTF correction method from the drop down menu. We like the ACE2 WeinerFilter Whole Image corrector.
12. Click on "Make Stack" 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.

Notes, Comments, and Suggestions:¶

1. Default parameters work well generally.
2. Remember that, if you low pass or high pass filter your stack particles, then any filters applied during subsequent processing will be in addition to this original filter. We tend to filter during alignment instead of during stack creation.

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