=========================================================================== 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 ===========================================================================