Appion

Looks great so far. Just two comments:
1. Tomography icon on myamiweb page does not take you to Appion pipeline but Leginon tomography parameter graphs. It is used to examine the behavior of tracking and modeling during the data collection.

2. If you can try a second cycle of protomo alignment by clicking "Setup Next Aligner Iteration", you will see it looks different from the first. See if you can figure out how to use the part on resetting alignment outside the tilt number part and make a figure regarding its behavior.

Thank you very much for doing this.

Hi, Anke,
1. Not sure which tab on which page you clicked to get this.
2. You might have noticed that runSubTomogram.php page does not let you specify the location of the subvolume in xy direction. It just ask how big you want it. This is because it uses particle selection run to get the center of "boxing" like any other appion image processing. The image in this case, is the z_project image created through full tomogram creation step.