https://github.com/azazellochg/eman

Scripts for EMAN2
https://github.com/azazellochg/eman

bash python

Last synced: about 1 month ago
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Scripts for EMAN2

• Host: GitHub
• URL: https://github.com/azazellochg/eman
• Owner: azazellochg
• License: gpl-3.0
• Created: 2014-05-06T15:20:42.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2019-01-10T11:39:48.000Z (almost 6 years ago)
• Last Synced: 2023-10-20T18:02:15.669Z (about 1 year ago)
• Topics: bash, python
• Language: Shell
• Size: 33.2 KB
• Stars: 4
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: change_box.sh
  • License: LICENSE.md

Awesome Lists containing this project

README

        
EMAN

====

EMAN conventions can be found here: https://github.com/azazellochg/3DEM-conventions/blob/master/eman2.md

### Scripts for EMAN2

##### FAQ

My list of frequently used commands / options in EMAN2.

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##### calculate_avg_std.py

Calculate average and standard deviation images for a stack of images (stack.hdf). I usually use it on a random set of 50-100 (non-)gain-corrected movies to check if gain reference was done properly.

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##### change_box.sh

The script will change box coordinates: apply coarse factor to downscale/upscale coordinates, change box size if requested, remove boxes too close to the mictrograph edge. New box files are in new_boxes folder.

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##### clean_boxes.sh

This script simply removes boxes that are too close to the micrograph edge.

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##### norm_corr.py

A simple script to do camera normalization correction (see Afanasyev et al., Scientific Reports 5, 2015), given a known avg and std images for the uncorrected movie stack

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##### xmipp3_to_eman_boxes

Simple script for coordinate conversion from XMIPP3 to EMAN (.pos to .box)