pdb2mrc

This program will generate a 3D electron density map from PDB files

pdb2mrc <pdb input> <mrc output> [info] [apix=<a/voxel>] [res=<resolution>] [box=<box size>] [het] [center] [solvate]

Parameters:


<pdb input>The PDB file to convert
<mrc output>The output file for the generated map
[info]If this is specified, information on the PDB file is displayed, no conversion is performed.
[apix=<a/voxel>]Angstroms per voxel in the output, default is 1
[res=<resolution>]Real space resolution, for 1/e width in F space multiply by 2.2
[box=<box size>]Box size in voxels, automatic if unspecified
[het]Include HET atoms in the conversion
[center]Center the model (center of charge)
[solvate]Solvate the model (with water). This is an approximate algorithm.

Usage:

pdb2mrc 1FAQ.pdb FAQ.mrc apix=1 res=1.5 center

Description

This will generate a 3D MRC map from a PDB file. This may be used by align3d or foldhunter, or for other purposes. The solvate option is better than that used by some other similar programs, but is NOT discrete water molecule solvation. It is still an approximate continuous method which still produces artifacts. In addition, without solvation, the program can generate models at any resolution, but with solvation, resolution must be 1.5 A or better.


EMAN Manual page, generated Mon Jan 10 15:41:45 2000