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This repo contains scripts for analyzing the position of flexibly attached subdomains with EM images. Protocol for analyzing flexibilty plotted onto 2D: 1. Merge columns from distance files into a single file: first file - distanceA_C; second file distanceB_C 2. Output MSA plt from header of sum3_10_150.img 3.'Select' avearages and membership info from classums stack: $ ./select_stack_msaPLT.py Usage: select_stack_msaPLT.py -p <plt file> -s <classums_stack> -b <boxed.lis file> Options: -h, --help show this help message and exit -p FILE PLT output file from msa classums header -s FILE msa classums stack -b FILE List of box files (ls *.box > boxed.lis) -d debug $ ./select_stack_msaPLT.py -p sum3_10_150.plt -s sum3_10_150.img -b boxed.lis This script will tell you run a proc2d command - do it to select 'good' averages. 4. Input parameters to create averages: $ ./make_subClass_dualAxes.py Usage: make_subClass_dualAxes.py -s <classums stack> -f <merged distances file> --topX=x --topY=y --botX=x --botY=y Options: -h, --help show this help message and exit -s FILE stack of selected, classified averages -f FILE Merged distances file --topX=FLOAT top left corner of box to use,x coordinate --topY=FLOAT top left corner of box to use,y coordinate --botX=FLOAT bottom right corner of box to use, x coordinate --botY=FLOAT bottom right corner of box to use, y coordinate -d debug $ ./make_subClass_dualAxes.py -s sum3_10_150_sel.img -f merge_distanceA_C_distanceB_C.spi --topX=12 --topY=28 --botX=20 --botY=24
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Scripts for focused classification of flexible subdomains
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