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DNA Script Usage

posted Nov 8, 2011, 11:07 AM by Dong Xu
DNA Generation and Manipulation script

dna.sh help prints this message
dna.sh <input file (.in)> Use a file as the input
dna.sh <output command> <dna commands>
    <output command> → -o <output pdb> | -o stdout
        output to a pdb file or standard out
    <dna commands> →  -c <dna command> [<dna commands>]
        define one or more dna commands
    <dna command> → <name to save to> <command>
        name must be uper or lower case characters
    <command> → read <input pdb> <chain in file>
            | generate <lowercase dna seqence> (A | B)
            | copy <name>
            | join <name> <residue number> <name>
            | modify <name> <operation>
            | print
    <operation> → rotate <source> <x rot> <y rot> <z rot>
            | translate <source> <delta x> <delta y> <delta z>
            | rotate_res <source> <residue to rotate about> <x rot> <y rot> <z rot>
            | center_res <source> <residue to center on>
            | align <source> <residue on source> <target chain> <residue on target> [<step> <step count>]

example:
dna.sh -o Temp.pdb \
-c F generate agtt A \
-c Q generate tcaagggtgtgatg B \
-c P generate tcaagggtgtgatg A \
-c R modify P rotate_res 5 120 -70 20 \
-c I join R 4 P \
-c F print \
-c I print \
-c Q print
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