PDB File Conversion: Converts an atomic model stored in a PDB file into a simulated electron density map. The coordinates (0,0,0) in PDB space will map to the center of the volume.

Usage in command line

sp_pdb2em.py  input_pdb  output_hdf  --apix=PIXEL_SIZE  --box=BOX_SIZE  --het  --chains=CHAIN_STRING --center=CENTERING_METHOD  --O  --tr0=MATRIX_FILE_PATH  --set_apix_value=PIXEL_SIZE_STRING  --quiet

sp_pdb2em does not support MPI.

sp_pdb2em.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]: Specify string of a single value (e.g. '256') to get a cubic box. Alternatively, use 'x,y,z' format to specify demensions of x,y,z-axis (e.g. '128,64,256'). 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. Note that GUI does not support the default mode. (default required string)

--het

Include hetero atoms: Otherwise, the HETATM entries in the PDB file are ignored. (default False)

--chains

Chain identifiers: A string list of chain identifiers to include (e.g. 'ABEFG'). By default, all chains will be included. (default none)

--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 from all PDB coordinates. 'n' - 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 by using O system of coordinates. (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)

--set_apix_value

Set header pixel size: Set pixel size in header of the ouput map. (default False)

--quiet

Silent mode: Does not print any information to the monitor. Verbose is the default. (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/sp_pdb2em.py

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

There are no known bugs so far.