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] [full] [allmdl] [sym=<cn|dn|icos>] [rot=<alt,az,phi>] [gen1] [sf=<filename>]

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>]Resolution defined in 'EM' way. reciprocal of the 1/2 width of a Gaussian in Fourier space
[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.
[full]Apply non-crystallographic symmetry (MTRIXs or BIOMTs) to get full structure
[allmdl]Ignore ENDMDL flags
[sym=<cn|dn|icos>]Apply additional symmetry to the structure
[rot=<alt,az,phi>]Apply rotation after symmetries are applied,
[gen1]This will generate density for only 1 copy of the molecule, but otherwise act as if all copies were generated.
[sf=<filename>]Generates the scattering structural factor curve

Usage:

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

Description

WARNING: the definition of resolution changed between build 34 and 35

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.

The purpose of [sym=] is mainly for generating full icosahedral virus structure, since the PDB files for some viruses (bluetongue virus) only have non-crystallographic symmetry transform matrix for half of the virus, we need to apply additional symmetry operation (for bluetongue virus use sym=c2) to generate the full structure. For bluetongue virus, the C2 is not enough, it requires another rotation along Z axis to make the the XYZ all on 2-fold axes, so [rot=] is added for this purpose to tranform the coordinates instead tranform of density map later on.

The solvate option works best with apix=.8 and res=2.4. The approximation becomes worse if res<3*apix. This will take some time to calculate, and is only an approximation.


EMAN Manual page, generated Wed Feb 18 10:33:43 2009