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Bug #2930

closed

zero degree particles are not centered

Added by Scott Stagg about 10 years ago. Updated almost 10 years ago.

Status:
Closed
Priority:
High
Assignee:
Category:
-
Target version:
-
Start date:
09/16/2014
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.1.0
Show in known bugs:
No
Workaround:

Description

We are having a bug where the zero degree tilt particles a stack for an RCT reconstruction are not centered. The tilted particles are centered fine, but the zero degree particles are systematically shifted to the lower right of the box. I have no idea where this is coming from. I have attached an image of the particle average


Files

average.png (5.1 KB) average.png Scott Stagg, 09/16/2014 11:44 AM
average.png (6.13 KB) average.png Neil Voss, 09/22/2014 01:29 PM

Related issues 2 (2 open0 closed)

Related to Appion - Bug #2939: Appion Developers Conference Call NotesNew09/24/2014

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Related to Appion - Bug #6530: Particle picks off center with K3 New01/11/2019

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Actions #1

Updated by Neil Voss about 10 years ago

Hi Scott, I saw the same problem. I have no idea. It could be when the particles go through tilt picker there is some transformation that is going off? Because the same picks before tiltPicker produce a centered stack.

Actions #2

Updated by Scott Stagg about 10 years ago

I haven't tracked it down in the code, but I'm sure you're right because I see the same behavior where before doing tilt pairs, the stack is centered.

Actions #4

Updated by Clint Potter about 10 years ago

  • Assignee set to Neil Voss
Actions #5

Updated by Neil Voss about 10 years ago

Hi Scott, just for clarification are the zero degree particles not centered or are the tilted particles not centered. In my case, the zero particles were fine, but the tilted ones were off center.

Anyway, have not had much time to track it down.

Actions #6

Updated by Scott Stagg about 10 years ago

I finished teaching and got my grant submitted and had a chance to look at this. I repeated what my postdoc was doing but with just one image. I am still getting the systematic offset, but I think I know what is going on. Neil, to answer your question, it is the untilted particles that are offset. I believe that which particles are offset depends on the order in which the images were collected. In my case, the tilted images were collected first followed by the untilted. The offset is happening during the tilt pair picking after the autorefinement step. I haven't confirmed this, but I think what is happening is that the model for the tilt geometry is causing the offset. I believe that the code is doing exactly what it should be doing, but this grid might be ever so slightly bent. Thus the the tilted images are fixed and the zero degree images are being adjusted to them based on the geometry model. Does this sound plausible? If so, I will close this issue.

Actions #7

Updated by Neil Voss about 10 years ago

Thanks for the feedback. There is an X and Y shift it must not be getting applied correctly during the commit for the second image. I have not had time to look at this, but hopefully soon.

Actions #8

Updated by Neil Voss about 10 years ago

  • Related to Bug #2939: Appion Developers Conference Call Notes added
Actions #9

Updated by Neil Voss almost 10 years ago

Did some testing today and tried to reproduce problem on 2 image set unsuccessfully. I still believe it is related to the shift in the tilt alignment parameters. Introducing a large shift in align and edit tilt picker did not produce problem.
Need to find a way to introduce a large shift into auto-tilt-aligner OR review the code.

Scott did you use auto-tilt-aligner OR align-and-edit tilt picker?

Actions #10

Updated by Neil Voss almost 10 years ago

  • Status changed from New to Assigned
Actions #11

Updated by Clint Potter almost 10 years ago

  • Status changed from Assigned to Closed
Actions #12

Updated by Scott Stagg almost 10 years ago

I believe this original problem was related to the specimen instead of the program. The poor centering happened with 3 different samples, then we got one sample where they matched very closely. I believe the original problem was happening because the sample was tilted so the geometry calculation wasn't working out accurately. After preparing a better sample, the problem went away.

Actions #13

Updated by Neil Voss almost 6 years ago

  • Related to Bug #6530: Particle picks off center with K3 added
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