## page was renamed from e2pdb2em
= Name =
sxpdb2em - PDB File Conversion: Converts an atomic model into a simulated density map 

= Usage =

''usage in command line''

sxpdb2em.py  input_pdb  output_hdf  --apix=pixel_size  --box=box_size  --het  --center=center  --O  --tr0=matrix_file  --quiet

=== Typical usage ===

sxpdb2em does not support MPI.

sxpdb2em.py  tRNA.pdb  tRNA.hdf  --apix=2.26  --box=150  --center=c  --O  --quiet  --tr0=<''filename''>  --het

== Input ==
    input_pdb:: Input PDB file: Starting atomic coordinates: (default required string)
    
    apix:: Pixel size of the output map [A]: (default 1.0)
    box:: Output box size [Voxels]: If not given, the program will find the minimum box size fitting the structure. Be aware that this will most likely result in a rectangular box. (default required int)
    het:: Include hetero atoms: Otherwise the HETATM entries in the PDB file are ignored. (default False)
    center:: Center model at the origin:: Specifies whether the atomic model should be moved to the origin before generating density map.  Available options are: c - Use the geometrical center of atoms; a - Use the center of mass (recommended); x,y,z - Vector to be subtracted for the coordinates. Default: no centering, in which case (0,0,0) in the PDB space will map to the center of the EM volume. (default n)
    O:: Apply additional rotation: This can be used to modify the orientation of the atomic model. (default False)
    tr0:: Rotational matrix file:: This file must contain the 3x4 transformation matrix to be applied to the PDB coordinates after centering. The translation vector (last column of the matrix) must be specified in Angstrom. (default none)

    * The remaining parameters are optional.
    quiet:: Silent mode: Does not print any information to the monitor. (default False)


== Output ==
    output_hdf:: Output map: (default required string)

= Description =
Thre program uses tri-linear interpolation.  Electron densities are taken to be equal to atomic masses.

= Author / Maintainer =
Pawel Penczek

= Keywords =
    category 1:: APPLICATIONS

= Files =
sxpdb2em.py

= Maturity =

Work perfectly well.
