[Chimera-users] fit map --nogui

[Thomas Goddard]

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)
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