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 ?
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 2.) Re-sample a map : Conserve the density map "box" size, and change the number of voxels that cover it
--Ben
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 > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
hi Ben - You can initiate a SampledDensityMap from a DensityHeader, which you can set to any dimension you want. Does that make sense ? Keren.
Our Ben - I am still for some reason not getting these messages, only after forwarding from Daniel :) On Aug 1, 2010, at 12:31 PM, Daniel Russel wrote:
> 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 >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
On Aug 1, 2010, at 10:07 PM, Keren Lasker wrote:
> hi Ben - > You can initiate a SampledDensityMap from a DensityHeader, which you can set to any dimension you want. > Does that make sense ? What fields of the density header must be set in order for construction to work right? set_number_of_voxels() set_resolution() set_{x,y,z}origin() Objectpixelsize_ (there doesn't seem to be a set function, right?) Anything else?
> Our Ben - I am still for some reason not getting these messages, only after forwarding from Daniel :) This message was old, I just revived it.
> On Aug 1, 2010, at 12:31 PM, Daniel Russel wrote: > >> 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 >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
Ben/Daniel - I agree that initializing a map from a bounding-box makes sense. Please see revision 1644 that now contains an example on how to do that em/examples/generate_density_map_of_fixed_dimension.py
I have added a function that generates a header from a bounding box and show how to use it in the example.
Keren. On Aug 2, 2010, at 7:57 AM, Daniel Russel wrote:
> On Aug 1, 2010, at 10:07 PM, Keren Lasker wrote: > >> hi Ben - >> You can initiate a SampledDensityMap from a DensityHeader, which >> you can set to any dimension you want. >> Does that make sense ? > What fields of the density header must be set in order for > construction to work right? > set_number_of_voxels() > set_resolution() > set_{x,y,z}origin() > Objectpixelsize_ (there doesn't seem to be a set function, right?) > Anything else? > > >> Our Ben - I am still for some reason not getting these messages, >> only after forwarding from Daniel :) > This message was old, I just revived it. > > >> On Aug 1, 2010, at 12:31 PM, Daniel Russel wrote: >> >>> 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 >>>> _______________________________________________ >>>> IMP-users mailing list >>>> IMP-users@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-users >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
Ben is currently using IMP 1.0 (as far as I know). Is the example likely to work on that? If so, Ben, you can just wait until tomorrow morning and then get it from the nightly build docs online.
On Aug 2, 2010, at 12:58 PM, Keren Lasker wrote:
> Ben/Daniel - > I agree that initializing a map from a bounding-box makes sense. > Please see revision 1644 that now contains an example on how to do that > em/examples/generate_density_map_of_fixed_dimension.py > > I have added a function that generates a header from a bounding box and show how to use it in the example. > > Keren. > On Aug 2, 2010, at 7:57 AM, Daniel Russel wrote: > >> On Aug 1, 2010, at 10:07 PM, Keren Lasker wrote: >> >>> hi Ben - >>> You can initiate a SampledDensityMap from a DensityHeader, which you can set to any dimension you want. >>> Does that make sense ? >> What fields of the density header must be set in order for construction to work right? >> set_number_of_voxels() >> set_resolution() >> set_{x,y,z}origin() >> Objectpixelsize_ (there doesn't seem to be a set function, right?) >> Anything else? >> >> >>> Our Ben - I am still for some reason not getting these messages, only after forwarding from Daniel :) >> This message was old, I just revived it. >> >> >>> On Aug 1, 2010, at 12:31 PM, Daniel Russel wrote: >>> >>>> 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 >>>>> _______________________________________________ >>>>> IMP-users mailing list >>>>> IMP-users@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-users >>>> >>>> _______________________________________________ >>>> IMP-users mailing list >>>> IMP-users@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-users >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
thanks Daniel. Ben please let me know which version you are using :) On Aug 2, 2010, at 1:01 PM, Daniel Russel wrote:
> Ben is currently using IMP 1.0 (as far as I know). Is the example > likely to work on that? If so, Ben, you can just wait until tomorrow > morning and then get it from the nightly build docs online. > > On Aug 2, 2010, at 12:58 PM, Keren Lasker wrote: > >> Ben/Daniel - >> I agree that initializing a map from a bounding-box makes sense. >> Please see revision 1644 that now contains an example on how to do >> that >> em/examples/generate_density_map_of_fixed_dimension.py >> >> I have added a function that generates a header from a bounding box >> and show how to use it in the example. >> >> Keren. >> On Aug 2, 2010, at 7:57 AM, Daniel Russel wrote: >> >>> On Aug 1, 2010, at 10:07 PM, Keren Lasker wrote: >>> >>>> hi Ben - >>>> You can initiate a SampledDensityMap from a DensityHeader, which >>>> you can set to any dimension you want. >>>> Does that make sense ? >>> What fields of the density header must be set in order for >>> construction to work right? >>> set_number_of_voxels() >>> set_resolution() >>> set_{x,y,z}origin() >>> Objectpixelsize_ (there doesn't seem to be a set function, right?) >>> Anything else? >>> >>> >>>> Our Ben - I am still for some reason not getting these messages, >>>> only after forwarding from Daniel :) >>> This message was old, I just revived it. >>> >>> >>>> On Aug 1, 2010, at 12:31 PM, Daniel Russel wrote: >>>> >>>>> 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 >>>>>> _______________________________________________ >>>>>> IMP-users mailing list >>>>>> IMP-users@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-users >>>>> >>>>> _______________________________________________ >>>>> IMP-users mailing list >>>>> IMP-users@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-users >>>> >>>> _______________________________________________ >>>> IMP-users mailing list >>>> IMP-users@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-users >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
Thanks a lot for your reactivity, and for the code adenda. I will test all you suggested ASAP.
Keren, for the moment I am effectively using IMP 1.0 binary for MAC OS X. I also svn-checkouted the repository in order to lurk'n learn from the sources, but did not compile it yet.
--Ben
Le 2 août 2010 à 22:04, Keren Lasker a écrit :
> thanks Daniel. > Ben please let me know which version you are using :) > On Aug 2, 2010, at 1:01 PM, Daniel Russel wrote: > >> Ben is currently using IMP 1.0 (as far as I know). Is the example likely to work on that? If so, Ben, you can just wait until tomorrow morning and then get it from the nightly build docs online. >> >> On Aug 2, 2010, at 12:58 PM, Keren Lasker wrote: >> >>> Ben/Daniel - >>> I agree that initializing a map from a bounding-box makes sense. >>> Please see revision 1644 that now contains an example on how to do that >>> em/examples/generate_density_map_of_fixed_dimension.py >>> >>> I have added a function that generates a header from a bounding box and show how to use it in the example. >>> >>> Keren.
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Benjamin SCHWARZ -
Daniel Russel -
Keren Lasker