logging.info('PDB reference map resolution: %.2f', args.resolution)
refbasename, refext = os.path.splitext(args.ref)
refoutput = refbasename + "_centered.pdb"
refside = side
voxel = (refside / movrho.shape)[0]
halfside = refside / 2
n = int(refside / voxel)
dx = refside / n
x_ = np.linspace(-halfside, halfside, n)
x, y, z = np.meshgrid(x_, x_, x_, indexing='ij')
xyz = np.column_stack((x.ravel(), y.ravel(), z.ravel()))
pdb = saxs.PDB(args.ref)
if args.center:
pdb.coords -= pdb.coords.mean(axis=0)
pdb.write(filename=refoutput)
refrho = saxs.pdb2map_gauss(pdb, xyz=xyz, sigma=args.resolution)
refrho = refrho * np.sum(movrho) / np.sum(refrho)
saxs.write_mrc(refrho, side, filename=refbasename + '_pdb.mrc')
if args.ref.endswith('.mrc'):
refrho, refside = saxs.read_mrc(args.ref)
if (not args.ref.endswith('.mrc')) and (not args.ref.endswith('.pdb')):
print "Invalid reference filename given. .mrc or .pdb file required"
sys.exit(1)
aligned = saxs.principal_axis_alignment(refrho, rho)
saxs.write_mrc(aligned, side, output + '.mrc')
print "%s.mrc written. " % (output, )
logging.info('END')
x,y,z = np.meshgrid(x_,x_,x_,indexing='ij')
xyz = np.column_stack((x.ravel(),y.ravel(),z.ravel()))
pdb = saxs.PDB(args.file)
if args.center:
pdboutput = basename+"_centered.pdb"
pdb.coords -= pdb.coords.mean(axis=0)
pdb.write(filename=pdboutput)
if n <= 20:
#n must be greater than 20 with current implementation of fast
#mode using KDTrees. So switch to slow mode, since its a small grid anyways
args.mode = "slow"
if args.mode == "fast":
rho = saxs.pdb2map_gauss(pdb,xyz=xyz,sigma=args.resolution,mode="fast",eps=1e-6)
elif args.mode == "slow":
rho = saxs.pdb2map_gauss(pdb,xyz=xyz,sigma=args.resolution,mode="slow")
else:
print "Note: Using FFT method results in severe truncation ripples in map."
print "This will also run a quick refinement of phases to attempt to clean this up."
rho, pdbidx = saxs.pdb2map_FFT(pdb,x=x,y=y,z=z,radii=None)
rho = saxs.denss_3DFs(rho_start=rho,dmax=side,voxel=dx,oversampling=1.,shrinkwrap=False,support=pdbidx)
print
saxs.write_mrc(rho,side,output+".mrc")