Name

sxpdb2em - convert atomic model (pdb file) into sampled electron density map

Usage

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

tRNA.pdb: pdb file with atomic coordinates.
apix: pixel size (in Angstrom) of the output map.
box: size of the output map in voxels. (If not given, the program will find the minimum box size that includes the structre. However, in most cases this will result in a rectangular box, i.e., each dimension will be different.)
center: specify whether to center the atomic model before converting to electron density map (warning: pdb deposited atomic models are not necesserily centered). Options: c - center using coordinates of atoms; a - center by setting center of gravity to zero (recommended); a triplet x,y,z (no spaces in between) - coordinates (in Angstrom) to be substracted from all the PDB coordinates. Default: no centering, in which case (0,0,0) in the PDB space will map to the center of the EM volume, i.e., (nx/2, ny/2, nz/2).
O: apply additional rotation so the model will appear in O in the same rotation as in chimera.
het: Include HET atoms in the map.
quiet: do not print any information to the monitor.
tr0: name of a file containing a 3x4 transformation matrix to be applied to the PDB coordinates after centering, prior to computing the density map. The translation vector (last column of the matrix) must be specified in Angstrom. If this parameter is omitted, no transformation is applied.

tRNA.hdf: output 3-D electron density map (any EM format). Attribute pixel_size will be set to the specified value.

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

Pawel Penczek

sxpdb2em.py

Work perfectly well.