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tar zxvf x3dna_md_v0.7.tar.gzand you will get a directory named x3dna_md_v0.7/, underneath you will find two Ruby scripts: x3dna_md.rb and extract_par.rb, and associated data files for testing and verification purpose.
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Usage:
x3dna_md.rb options
Examples:
x3dna_md.rb -b bpfile.dat -e sample_md0.pdb
# 21 models (0-21); output (default): 'x3dna_md.out'
# also generate 'model_list.dat', see below
x3dna_md.rb -b bpfile.dat -m model_list.dat -o x3dna_md2.out
# diff x3dna_md.out x3dna_md2.out
x3dna_md.rb -b bpfile.dat -p 'pdbdir/model_*.pdb' -o x3dna_md3.out
# note the quote for -p option; 20 models (1-20)
# also also generate 'pdb_list.dat', see below
x3dna_md.rb -b bpfile.dat -l pdb_list.dat -o x3dna_md4.out
# diff x3dna_md3.out x3dna_md4.out
# note the order of PDB files: 1, 10..19, 2, 20, 3..9
Options:
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--bpfile, -b <s>: File containing base-pairing info (as generated
from find_pair, and EDITED as appropriate)
--outfile, -o <s>: Output file name (default: x3dna_md.out)
--ensemble, -e <s>: Model ensemble in pairs
--models, -m <s>: Explicit list of model numbers
--pattern, -p <s>: Pattern of PDB files to process (e.g., *.pdb)
--list, -l <s>: Explicit list of individual PDB file
--version, -v: Print version and exit
--help, -h: Show this message
Note specifically that an input file with base-pairing (-b) information must be provided, which can be easily generated using find_pair and then manually edited as necessary. Needless to say, the base-pair file specified with -b must match the pairing configuration in each model of the ensemble. The input can be conveniently supplied with one of four options (-e, -m, -p, -l), allowing for great flexibility. Importantly, for the -e and -m options, each model in the ensemble must be delimited by an MODEL/ENDMDL pair, as clearly documented in the Coordinate Section of the PDB format (http://www.wwpdb.org/documentation/format32/sect9.html).
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Usage:
extract_par.rb options
Examples:
extract_par.rb -l
# to see a list of all parameters
extract_par.rb -p prop
# -p 36 also fine (see above); from file 'x3dna_md.out'
# for propeller, no need to specify full: -p pr suffices
extract_par.rb -p slide -s , -f x3dna_md3.out
# comma separated, from file 'x3dna_md3.out', to screen
extract_par.rb -p roll -s ' ' -n > roll.dat
# space separated, no row-label, to file 'roll.dat'
extract_par.rb -a
# extract all parameters, each in a separate file
# prefixed with 'x3dna_md_': e.g., 'x3dna_md_chi1.out'
# run 'extract_par.rb -c' to clean up all generated files
extract_par.rb -e 1 -p chi1
# extract the chi torsion angle of strand I, but exclude
# those from the two terminal base pairs. For comparison,
# run also: extract_par.rb -p chi1
Options:
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--no-1col, -n: Delete the first annotation column
--separator, -s <s>: Separator for fields [tab] (default: )
--list, -l: List all parameters
--all, -a: Extract all parameters into separate files
--clean, -c: Clean up parameter files by the above -a option
--par-name, -p <s>: Name of parameter
--fromfile, -f <s>: File name with parameters (default:
x3dna_md.out)
--end-effects, -e : No. of end pairs to ignore (default: 0, 0)
--version, -v: Print version and exit
--help, -h: Show this message
Three sample output files are attached below for reference: propeller.tsv contains propeller of 21 models of a 12-mer in the default tab-delimted format; slide.csv contains roll in comma separated format; and roll.dat in space separated format, without leading label column. The output parameter table is intended to be fed into R/Matlab/Octive/Excel etc for statistical analysis or visualization.Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.