Name

e2pdb2em - convert atomic model (pdb file) into sampled electron density map

Usage

e2pdb2em.py tRNA.pdb tRNA.hdf --apix=2.26 --box=150 --center=c --O

tRNA.pdb: pdb file with atomic coordinates
apix: pixel size in Angstroms 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) (default no centering).
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.
chains: String list of chain identifiers to include, e.g., chains='ABEFG'
quiet: do not print any information to the monitor.

tRNA.hdf: output 3-D electron density map (any EM format). Attribute Pixel_size will be set tot he specified value.

Thre program uses Gaussian kernel to interpolate atomic coordinates on the 3D grid. Electron densities are taken to be equal to atomic masses.

Steve Ludtke

EMAN2/src/eman2/programs/e2pdb2em.py

under development: new features will be added. In particular, please do not use option res!