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NAME
rotate_mol - reorient a structure in PDB or ALCHEMY format
SYNOPSIS
rotate_mol [OPTION] INPFILE OUTFILE
DESCRIPTION
change the orientation of a structure data file in PDB or ALCHEMY
and write the result in a new file. The new orientation can be from
RasMol, a user-defined rotation matrix or be based on the principle
moment of inertia
-c move the structure to its geometric center
-a set structure with regard to the principle moment of inertia
based on ALL atoms
-b same as -a, but based on only BASE atoms [default]
-p same as -a, but based on only PROTEIN atoms
-t=TRNSMAT data file containing Transformation matrix (rotmat.dat)
-r=ROTFILE file of Rotation angles as from RasMol (to molscript)
-h this help message (any non-recognized options will do)
INPUT
PDB or ALCHEMY data file
EXAMPLES
Use RasMol to load a structure and rotate it to get your preferred
view, then issue "write molscript my_view.scr" in command window
rotate_mol -c my_view.scr sample.pdb sample_view.pdb
rotate_mol -b sample.pdb sample_bpmi.pdb
rotate_mol -m rotmat.dat sample.pdb sample_rmat.pdb
OUTPUT
output structure file in new view
pmiview1, pmiview2, pmiview3, rotmat.dat
SEE ALSO
r3d_atom, blocview, frame_mol
AUTHOR
Written by Xiang-Jun Lu at Wilma K. Olson Laboratory at Rutgers
Check URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/
Report bugs to
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