PDB File Conversion: Converts an atomic model into a simulated density map.

Usage in command line

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

sxpdb2em does not support MPI.

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

input_pdb

Input PDB file: Starting atomic coordinates. (default required string)

output_hdf

Output map: Specify file path for output map. (default required string)

--apix

Pixel size of output map [A]: 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 3×4 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)

--quiet

Silent mode: Does not print any information to the monitor. (default False)

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

Pawel A. Penczek

Category 1:: APPLICATIONS

sparx/bin/sxpdb2em.py

Stable:: Has been evaluated and tested. Please let us know if there are any bugs.

There are no known bugs so far.