cvtpdb

NAME

     cvtpdb - converts a pdb file  between  Cartesian  and  frac-
     tional  coordinates,  vice-versa, and coordinate transforma-
     tions.

USAGE

     cvtpdb crystal [-f | -c |  -t  |  -r  |  -e]  <  file.pdb  >
     newfile.pdb


     -f   convert from fractional to Cartesian.

     -c   convert from Cartesian to fractional.

     -t vx vy vz
          translate by the amount specified in vx vy vz.

     -r r11 r12 r13 r21 r22 r23 r31 r32 r33
          rotate by matrix

     -e q1 q2 q3
          rotate by the Eularian angles q1, q2, q3.

DISCUSSION

     Note the nonstandard use of  crystal  on  the  command  line
     instead  of reading from the environment. This forces you to
     think carefully, since it is critical for correct operation.
     Converting  to  fractional  coordinates is especially useful
     when  applying   crystallographic   transformations.   After
     transformation,  convert back to Cartesian. You can pipe the
     output of  one  cvtpdb  into  another  to  chain  operations
     together.  For  example  to  generate  the  second  symmetry
     related molecule in P21 (-x, y+1/2, -z) and translate it  to
     the unit cell at +1, 0, -1:

cvtpdb crystal -f

cvtpdb crystal -r -1 0 0 0 1 0 0 0 -1 |\ !rotate by -x,y,-z

cvtpdb crystal -t 0 .5 0 |\ !translate by x, y+1/2, z)

cvtpdb crystal -t 1 0 1 |\ !translate by +1, 0 -1

cvtpdb crystal -c > molecule2.pdb !convert back to Cartesian

     Such a complicated command is best done in a shell file  and
     is very handy for generating packing diagrams.

VERSION

     Release 3.2 of XtalView

SEE ALSO

     xtalview(1)