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Task #621

closed

Appion User Guide: Tomography

Added by Anke Mulder almost 14 years ago. Updated over 13 years ago.

Status:
Closed
Priority:
High
Assignee:
Anchi Cheng
Category:
Documentation
Target version:
Appion/Leginon 2.0.0
Start date:
06/03/2010
Due date:
% Done:

50%

Estimated time:

Description

Documenation

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 #1

Updated by Anke Mulder almost 14 years ago

  • Status changed from New to Assigned
  • Assignee changed from Anke Mulder to Anchi Cheng
  • % Done changed from 0 to 50

Anchi. Can you take a quick look at the documentation I have for Tomography so far? Let me know if I need to take a different direction, or have gotten anything wrong.

Thanks!
a.

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 #2

Updated by Anchi Cheng almost 14 years ago

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.

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 #3

Updated by Anchi Cheng almost 14 years ago

  • Assignee changed from Anchi Cheng to Anke Mulder
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 #4

Updated by Anke Mulder almost 14 years ago

  • Assignee changed from Anke Mulder to Anchi Cheng

Hi Anchi. I made the changes as requested. Please check to see if I make sense!

Other:
1. When I click on "tomography" from the appion processing page, it takes me to the userguide page for tomography... not sure what was meant by redirecting to leginon pages?...
2. I tried running the upload tomogram function, and it says one complete, but I still cannot create subvolumes... it claims that I haven't selected a particle stack. what does this mean?

Thanks!
a.

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 #5

Updated by Anchi Cheng almost 14 years ago

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.

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 #6

Updated by Anchi Cheng almost 14 years ago

  • Assignee changed from Anchi Cheng to Anke Mulder
  • Priority changed from Immediate to High
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 #7

Updated by Anke Mulder almost 14 years ago

  • Assignee changed from Anke Mulder to Anchi Cheng

The following sections need to be finished:

Create tomogram subvolume: I have a good start, but we still need steps detailing the picking of sub-tomograms, etc.
Average tomogram subvolumes: This needs to be written

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 #8

Updated by Anchi Cheng over 13 years ago

  • Status changed from Assigned to Closed
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