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Feature #1436

open

helical rotation in a single interpolation

Added by Neil Voss about 13 years ago. Updated about 13 years ago.

Status:
Assigned
Priority:
Normal
Assignee:
Category:
-
Target version:
-
Start date:
09/28/2011
Due date:
% Done:

0%

Estimated time:

Description

I'm working on getting stack creation to do the helical rotation in a single interpolation, but I was wondering if I could enlist your help to figure out how incorporate this with your new apBoxer stuff. Right now the way I find the best angle is diffract each filament and rotate them through a range of fine angles until the intensity at the equator is maximized. I have a C shell script to do this, but I'm trying to figure out which stage to insert it in the python scripts. If I put it in makestack2.py after apBoxer.boxerRotate, then the roughly rotated stack will need to be broken up into mrc files, run through my script to get the fine angle for each filament, then the 2 angles can be combined, and apBoxer rerun with the final angles so it applies only a single interpolation. The problems I see with this are it's clunky (writing a stack, breaking it up, and rewriting it), and it's a little tricky getting the angles from my c shell script back into python (the only way I see to do this is write it to a text file and read the angles in). It would be much cleaner and easier if the second angle could be found in boxerRotate and added with the first angle before the stack was written, but I don't know how to do this with an image array. Is there a way to write the array to an mrc file, run the c shell script to find the final angle, then recalculate the array before writing it to the stack? Do you have any thoughts or suggestions on the best way to tackle this? Thanks so much!!

~Lauren

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