Keren? I have comments below.

On Jul 22, 2010, at 6:51 AM, Benjamin SCHWARZ wrote:

Hi list,

    I could not find how to Generate a density map from a structure with a *fixed* dimension :

When using IMP.em.SampledDensityMap(ps,resolution,apix) with a fixed size for apix, the grid size depends on the resolution. I would like to write a function that would allow me to generate maps with the same number of vertices (and the same space coverage) for different resolutions. I thus tried :

def pdbFile2dmap (pdbStream,densityFile,resolution,apix,sel,bboxCoverage=1.2):

    '''

    pdbStream       : where to read the structure

    densityFile     : name of the file where to drop the density map

    resolution      : resolution of the density map

    apix            : voxel size

    sel             : selector for reading structure

    bboxCoverage    : approximate bbox coverage of the density map 

    '''

    m= IMP.Model()

    # read protein

    mh              = IMP.atom.read_pdb(pdbStream,m,sel)

    # add radius info to each atom

    IMP.atom.add_radii(mh)

    # compute bbox, and map size in voxels

    bbox            = IMP.atom.get_bounding_box(mh)

    diag            = bbox.get_corner(0) - bbox.get_corner(1)

    nx              = int(bboxCoverage * diag[0] / apix)

    ny              = int(bboxCoverage * diag[1] / apix)

    nz              = int(bboxCoverage * diag[2] / apix)

    # compute origin

    origin          = bbox.get_corner(0) + (1-bboxCoverage)/2 * diag

    dmap            = IMP.em.SampledDensityMap()

#    dmap.CreateVoidMap(nx,ny,nz)

    ps              = IMP.Particles(IMP.core.get_leaves(mh))

    dmap.set_particles(ps)

    dmap.set_origin(origin)

    dmap.get_header_writable().set_number_of_voxels(nx,ny,nz)

    dmap.get_header_writable().set_resolution(resolution)

    dmap.update_voxel_size(apix)

    dmap.resample()

    dmap.calcRMS()      # computes statistic stuff about the map and insert it in the header

    print dmap.get_header().show(),"\n"

    IMP.em.write_map(dmap,densityFile,IMP.em.MRCReaderWriter())

that resulted in :

python(10802) malloc: *** mmap(size=18446744073709314048) failed (error code=12)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

Traceback (most recent call last):

  File "./pdb2density.py", line 181, in <module>

    pdbFile2dmap(pdbStream,densityFile,resolution,apix,sel,1.2)

  File "./pdb2density.py", line 75, in pdbFile2dmap

    dmap.update_voxel_size(apix)

  File "/usr/local/lib/python2.6/site-packages/IMP/em/__init__.py", line 428, in update_voxel_size

    def update_voxel_size(self, *args): return _IMP_em.DensityMap_update_voxel_size(self, *args)

MemoryError: std::bad_alloc

Can you tell me if my approach is OK, and how to solve my allocation problem ?

There DenistyMap/DensityHeader is still a bit finicky (that is, there are protocols which have to be followed, and, even worse, they don't tend to be documented). Keren is working on a cleaner version. My guess it the problem is due to not setting the "upper right" value or the length of the edge of each voxel. I don't see the function to do that offhand. Keren?

I would also like to know if there are easy means in IMP to 

1.) Strip a density map : out of an existing map, create a new map or restrict the existing one, so as to conserve only a central subset of voxels

There is get_transformed_into() which could be used. This may be a post 1.0 addition.

2.) Re-sample a map : Conserve the density map "box" size, and change the number of voxels that cover it

There is get_resampled(). Also may be a post 1.0 addition.

 

   --Ben

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