Hello, I am having some problems using/adapting a script I found by searching the mailing list. The script is pasted below but to summarize it should print out the transformation matrix used to fit one map to another. In principle I would like to do the same but in addition to writing out the matrix I would also like to apply it and save the resulting map. I am currently using chimera 1.4 build 27496 (Aqua on OSX 10.5.7) the first problem I have is just invoking the python interpreter..... if I use: Chimera.app/Contents/MacOS/chimera --nogui fittomap.py Executing fittomap.py... Traceback (most recent call last): File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ __main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimeraInit.py", line 407, in init chimera.openModels.open(a, prefixableType=1) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimera/__init__.py", line 1357, in open models = func(filename, *args, **kw) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimera/__init__.py", line 794, in _openPython loadFunc(sandboxName, fileName, f) File "fittomap.py", line 70, in <module> fit_map_in_map(p1, p2) File "fittomap.py", line 24, in fit_map_in_map from VolumeViewer import Data_Region, full_region, Rendering_Options ImportError: cannot import name Data_Region Error while processing fittomap.py: ImportError: cannot import name Data_Region (see reply log for Python traceback info) # ----------------------------------------------------------------------------- # Example script for fitting one map in another without the graphical user # interface. # # chimera --nogui fitnogui.py # # It can also be run using the graphical Chimera interface using File/ Open. # def fit_map_in_map(map1_path, map2_path, initial_map1_transform = None, map1_threshold = None, ijk_step_size_min = 0.01, # Grid index units ijk_step_size_max = 0.5, # Grid index units max_steps = 100, optimize_translation = True, optimize_rotation = True): # Files have to have file suffix indicating volume format. from VolumeData import open_file data1 = open_file(map1_path) data2 = open_file(map2_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map1 = Data_Region(data1, full_region(data1.size), '', ro) map2 = Data_Region(data2, full_region(data2.size), '', ro) if initial_map1_transform: from PDBmatrices.matrices import chimera_xform xf = chimera_xform(initial_map1_transform) map1.surface_model().openState.globalXform(xf) use_threshold = (map1_threshold != None) from FitMap import map_points_and_weights, motion_to_maximum points, point_weights = map_points_and_weights(map1, use_threshold) if len(points) == 0: if use_threshold: print 'No grid points above map threshold.' else: print 'Map has no non-zero values.' return move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps, ijk_step_size_min, ijk_step_size_max, optimize_translation, optimize_rotation) if initial_map1_transform: from PDBmatrices.matrices import multiply_matrices move_tf = multiply_matrices(move_tf, initial_map1_transform) header = ('\nFit map %s in map %s using %d points\n' % (map1.full_name(), map2.full_name(), stats['points']) + ' correlation = %.4g, overlap = %.4g\n' % (stats['correlation'], stats['overlap']) + ' steps = %d, shift = %.3g, angle = %.3g degrees\n' % (stats['steps'], stats['shift'], stats['angle'])) print header from FitMap.gui import transformation_description tfs = transformation_description(move_tf) print tfs # ----------------------------------------------------------------------------- # Example call fitting map into itself. # p1 = p2 = '/usr/local/src/chimera-demos/volume/examples/groel.mrc' fit_map_in_map(p1, p2)
Hi Sean, That fitnogui.py script from 2 years ago is not compatible with the current Chimera 1.4. Here's an updated version of the script http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts The Chimera fitting only does a local optimization so the starting position has to be close to the correct fit for it to work. To write the fit map out in the new orientation you have to interpolate it on a new grid because the map file formats don't support specifying a rotation of the coordinate system. There is a Chimera command to do that "vop" (volume operation). For example if map #1 has been fit to map #0 the following commands will interpolate the new map #1 placement at the grid points of map #0 and save the resulting map (#5) to a new file. vop #1 resample onGrid #0 modelId 5 volume #5 save /tmp/newmap.mrc Here's documentation http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html You can run such commands from Python as follows. from chimera import runCommand as r r('vop #1 resample onGrid #0 modelId 5') Unfortunately there is not a Chimera command for the fitting that would allow you to avoid the Python altogether. There is a command in Chimera 1.4 daily builds to report the rotation/translation of one model relative to another measure rotation #0 #1 Matrix rotation and translation 1.00000000 -0.00008162 0.00004438 0.00003441 0.00008162 1.00000000 -0.00001398 -0.00008961 -0.00004438 0.00001398 1.00000000 0.00031721 Axis 0.14880493 0.47238450 0.86874045 Axis point 2.47734414 -0.01307674 0.00000000 Rotation angle (degrees) 0.00538331 Shift along axis 0.00023836 The measure command is described here http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html Tom sean connell wrote:
Hello, I am having some problems using/adapting a script I found by searching the mailing list. The script is pasted below but to summarize it should print out the transformation matrix used to fit one map to another. In principle I would like to do the same but in addition to writing out the matrix I would also like to apply it and save the resulting map. I am currently using chimera 1.4 build 27496 (Aqua on OSX 10.5.7)
the first problem I have is just invoking the python interpreter..... if I use:
Chimera.app/Contents/MacOS/chimera --nogui fittomap.py Executing fittomap.py... Traceback (most recent call last): File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ __main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimeraInit.py", line 407, in init chimera.openModels.open(a, prefixableType=1) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimera/__init__.py", line 1357, in open models = func(filename, *args, **kw) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimera/__init__.py", line 794, in _openPython loadFunc(sandboxName, fileName, f) File "fittomap.py", line 70, in <module> fit_map_in_map(p1, p2) File "fittomap.py", line 24, in fit_map_in_map from VolumeViewer import Data_Region, full_region, Rendering_Options ImportError: cannot import name Data_Region Error while processing fittomap.py: ImportError: cannot import name Data_Region (see reply log for Python traceback info)
# ----------------------------------------------------------------------------- # Example script for fitting one map in another without the graphical user # interface. # # chimera --nogui fitnogui.py # # It can also be run using the graphical Chimera interface using File/ Open. # def fit_map_in_map(map1_path, map2_path, initial_map1_transform = None, map1_threshold = None, ijk_step_size_min = 0.01, # Grid index units ijk_step_size_max = 0.5, # Grid index units max_steps = 100, optimize_translation = True, optimize_rotation = True):
# Files have to have file suffix indicating volume format. from VolumeData import open_file data1 = open_file(map1_path) data2 = open_file(map2_path)
from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map1 = Data_Region(data1, full_region(data1.size), '', ro) map2 = Data_Region(data2, full_region(data2.size), '', ro)
if initial_map1_transform: from PDBmatrices.matrices import chimera_xform xf = chimera_xform(initial_map1_transform) map1.surface_model().openState.globalXform(xf)
use_threshold = (map1_threshold != None)
from FitMap import map_points_and_weights, motion_to_maximum points, point_weights = map_points_and_weights(map1, use_threshold)
if len(points) == 0: if use_threshold: print 'No grid points above map threshold.' else: print 'Map has no non-zero values.' return
move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps, ijk_step_size_min, ijk_step_size_max, optimize_translation, optimize_rotation)
if initial_map1_transform: from PDBmatrices.matrices import multiply_matrices move_tf = multiply_matrices(move_tf, initial_map1_transform)
header = ('\nFit map %s in map %s using %d points\n' % (map1.full_name(), map2.full_name(), stats['points']) + ' correlation = %.4g, overlap = %.4g\n' % (stats['correlation'], stats['overlap']) + ' steps = %d, shift = %.3g, angle = %.3g degrees\n' % (stats['steps'], stats['shift'], stats['angle'])) print header
from FitMap.gui import transformation_description tfs = transformation_description(move_tf) print tfs
# ----------------------------------------------------------------------------- # Example call fitting map into itself. # p1 = p2 = '/usr/local/src/chimera-demos/volume/examples/groel.mrc' fit_map_in_map(p1, p2) _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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sean connell -
Thomas Goddard