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