3DNA commands

$ find_pair 
===========================================================================
NAME
        find_pair - locate base-pairs and helical regions
SYNOPSIS
        find_pair [OPTION] PDBFILE OUTFILE
DESCRIPTION
        locate base-pairs and helical regions given a PDB data file. Its
        output can be directly fed into analyze, cehs and Lavery's Curves
        program.
        -s, -1  treat the whole structure as a continuous single helix.
                Useful for getting all backbone torsion angles
        -c      get Curves input for a duplex
        -c+     get input for Curves+ (duplex, ATOM records only)
        -d      generate a separate output file for each helical region
        -p      find all base-pairs and higher-order base associations
        -a      read in only the ATOM records, ignoring HETATM records
        -z      more detailed base-pairing information in the output
        -h      this help message (any non-recognized options will do)
INPUT
        PDB data file
        One-letter options can be in either case, any order and combined
EXAMPLES
        find_pair sample.pdb sample.inp
        find_pair -p sample.pdb allbp_list
        find_pair -c+ sample.pdb sample_c+.inp
                  [then run: Cur+ < sample_c+.inp]
OUTPUT
        base-pair listing for input to analyze, cehs and Curves
        bestpairs.pdb, hel_regions.pdb, col_chains.scr, col_helices.scr
        allpairs.pdb, multiplets.pdb, mulbp.inp
SEE ALSO
        analyze, cehs, anyhelix, ex_str, stack2img
AUTHOR
        3DNA v2.1 (2013), created and maintained by Xiang-Jun Lu (PhD)


Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/


 x3dna_ensemble extract -h
------------------------------------------------------------------------
Extract 3DNA structural parameters of an ensemble of NMR structures or
MD trajectories, after running 'x3dna_ensemble analyze'. The extracted
parameters are intended to be exported into Excel, Matlab and R etc for
further data analysis/visualization.

Usage:
        x3dna_ensemble extract options
Examples:
        x3dna_ensemble extract -l
             # to see a list of all parameters
        x3dna_ensemble extract -p prop
             # for propeller, no need to specify full: -p pr suffices
             # -p 36 also fine (see above); use 'ensemble_example.out'
        x3dna_ensemble extract -p slide -s , -f ensemble_example3.out
             # comma separated, from file 'ensemble_example3.out'
        x3dna_ensemble extract -p roll -s ' ' -n -o roll.dat
             # space separated, no row-label, to file 'roll.dat'
        x3dna_ensemble extract -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: x3dna_ensemble extract -p chi1
        x3dna_ensemble extract -a
             # extract all parameters, each in a separate file
Options:
------------------------------------------------------------------------
  --separator, -s :   Separator for fields [\t] (default: )
   --par-name, -p :   Name of parameter to extract
   --fromfile, -f :   Parameters file (default: ensemble_example.out)
    --outfile, -o :   File of selected parameter (default: stdout)
   --end-bps, -e :   Number of end pairs to ignore (default: 0, 0)
            --all, -a:   Extract all parameters into separate files
          --clean, -c:   Clean up parameter files by the -a option
           --list, -l:   List all parameters
        --no-1col, -n:   Delete the first (label) column
           --help, -h:   Show this message

x3dna_ensemble analyze -h

------------------------------------------------------------------------

Analyze a MODEL/ENDMDL delineated ensemble of NMR structures or MD

trajectories. All models must correspond to different conformations

of the same molecule. For the analysis of duplexes (default), a template

base-pair input file, generated with 'find_pair' and manually edited

as necessary, must be provided.

Usage:

        x3dna_ensemble analyze options

Examples:

        x3dna_ensemble analyze -b bpfile.dat -e sample_md0.pdb

             # 21 models (0-20); output (default): 'ensemble_example.out'

             # also generate 'model_list.dat', see example below

        x3dna_ensemble analyze -b bpfile.dat -m model_list.dat -o ensemble_example2.out

             # diff ensemble_example.out ensemble_example2.out

        x3dna_ensemble analyze -b bpfile.dat -p 'pdbdir/model_*.pdb' -o ensemble_example3.out

             # note to quote the -p option; 20 models (1-20)

             # also generate 'pdb_list.dat', see example below

        x3dna_ensemble analyze -b bpfile.dat -l pdb_list.dat -o ensemble_example4.out

             # diff ensemble_example3.out ensemble_example4.out

             # note the order of the models: 1, 10..19, 2, 20, 3..9

        x3dna_ensemble analyze -s -e sample_md0.pdb

             # perform a 'single'-stranded analysis

        x3dna_ensemble analyze -t -e sample_md0.pdb

             # calculate all 'torsion' angles

        find_pair 355d.pdb 355d.bps

        x3dna_ensemble analyze -b 355d.bps --one 355d.pdb

             # process the structure file 355d.pdb specified in 355d.bps

Options:

------------------------------------------------------------------------

    --bpfile, -b :   Name of file containing base-pairing info

   --outfile, -o :   Output file (default: ensemble_example.out)

        --single, -s:   Single-stranded DNA/RNA

       --torsion, -t:   Torsion angles

          --ring, -r:   Base ring center & normal vector

  --ensemble, -e :   Ensemble delineated with MODEL/ENDMDL pairs

    --models, -m :   File containing an explicit list of model numbers

   --pattern, -p :   Pattern of model files to process (e.g., *.pdb)

      --list, -l :   File containing an explicit list of models

       --one, -n :   One regular structure [special case]

          --info, -i:   Show only model info in the ensemble [with -e]

          --help, -h:   Show this message