Fit to Segments

Fit to Segments rigidly fits atomic structures into segmentation regions from Segment Map. Along with that tool, it is part of the Segger package described in:

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC. J Struct Biol. 2010 Jun;170(3):427-38.

There are several ways to start Fit to Segments, a tool in the Volume Data category (including from the Volume Viewer Tools menu).

The Structure to fit should be chosen from the pulldown menu of molecule models. Any atoms in the model that are not desired for fitting, such as solvent or extra chains, should be deleted before the fitting is done.

Clicking Fit performs the fitting. The default settings are to fit the structure to the selected regions using the principal axes method. The regions are made transparent; region transparency/opacity can be adjusted further using the Regions menu in Segment Map or the main Chimera menu Actions... Surface.

Fit information is shown in a table:

• Corr - the correlation, also known as the cross-correlation score, between the map within the segmentation region(s) used for fitting and the map generated from the atomic structure
• Molecule - the chosen structure
• Map - the density map from which the segmentation region(s) were derived
• Region - the segmentation region(s) used for fitting

• Density map resolution [r] grid spacing [s] - set parameters for generating a density map from the atomic structure, to allow calculating correlation values for fits. Each atom is described as a 3D Gaussian distribution of width proportional to the resolution r and amplitude proportional to the atomic number (as is done by the command molmap). The grid spacing s is the separation of points along the X, Y, and Z axes of the generated map. The resolution and spacing should be approximately the same as for the map into which the structure is being fit (the map that was segmented). Clicking Fit or Calculate Map will generate the map from the structure if it does not already exist.
  
  
• Which regions to use for fitting:
  • Combined selected regions (default) - use the selected sementation regions collectively
  • Each selected region - use each selected segmentation region for a separate fit
  • Groups of regions including selected region - generate groups of segmentation regions that include the selected one, try fitting to each group; save the best fits in the table
  • Groups of regions including all regions - combinatorially group subsets of all segmentation regions, try fitting to each group; save the best fits in the table
  
  
• Alignment method:
  • Align principal axes (faster) (default) - align centers, then principal axes from longest to shortest. The center and principal axes of a structure are calculated from its atomic coordinates, non-mass-weighted. The center and principal axes of a region or group of regions are calculated from the voxels they enclose; all grid points inside the surface(s) are weighted equally. The principal axes are the eigenvectors of a covarience matrix. An eigenvector gives the direction of each axis, but the signs of these directions are ambiguous. When performing the alignment, the signs are flipped to generate four possible transforms. Only non-reflecting transforms are considered, in which either none or two of the three axes are flipped. The fit with the highest correlation is kept.

    The principal axes of the atomic structure can be shown/hidden with the File menu in Fit to Segments. The principal axes of segmentation regions can be shown with the Regions menu in Segment Map.

  • Rotational search (more reliable) - align centers, then exhaustively rotate the structure to find the best fit. The alignment with the highest correlation is kept.
    
    
  • Optimize fits (on by default) - whether to perform a local optimization of each fit. Optimization uses density both inside and outside the region(s) used in the initial fit, and can move the structure far from the region(s).

• Save chosen fit molecules - save a PDB file of the structure in its fit position for each chosen row in the table of fits

• Place molecule copies - add a copy of the structure in its fit position (as a new model) for each chosen row in the table of fits
• Delete fits from list - remove the chosen row(s) from the table of fits

• Show molecule axes - display the principal axes of the atomic structure as arrows
• Hide molecule axes - hide the principal axes of the atomic structure
• Show overlapping regions - display only the regions that overlap the atomic structure in its current position (all regions can be displayed again using the Regions menu in Segment Map)