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generate_density_map_of_fixed_dimension.py
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## \example em/generate_density_map_of_fixed_dimension.py
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## Shows how to generate a density map of fixed dimension and how to sample particles within this density map.
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import
IMP
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import
IMP.atom
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import
IMP.em
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m=
IMP.Model
()
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#1. read a protein and get its bounding box dimension
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sel=
IMP.atom.CAlphaPDBSelector
()
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# read protein
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mh=
IMP.atom.read_pdb
(
IMP.em.get_example_path
(
"input.pdb"
),m,sel)
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apix=1.
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resolution=6.
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# compute bbox, and map size in voxels
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bbox =
IMP.atom.get_bounding_box
(mh)
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#diag = bbox.get_corner(0) - bbox.get_corner(1)
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#nx = int(bboxCoverage * diag[0] / apix)
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#ny = int(bboxCoverage * diag[1] / apix)
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#nz = int(bboxCoverage * diag[2] / apix)
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#create a density header of the requested size
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dheader =
IMP.em.create_density_header
(bbox,apix)
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dheader.set_resolution(resolution)
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dmap =
IMP.em.SampledDensityMap
(dheader)
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ps =
IMP.core.get_leaves
(mh)
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dmap.set_particles(ps)
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#dmap.get_header_writable().set_number_of_voxels(nx,ny,nz)
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dmap.resample()
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dmap.calcRMS()
# computes statistic stuff about the map and insert it in the header
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print
dmap.get_header().
show
(),
"\n"
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IMP.em.write_map
(dmap,
"map.mrc"
,
IMP.em.MRCReaderWriter
())