MultiFit Help Pages

• Input Fields
• Output
• Examples
• Related Resources

Input Fields

• Email

  If set, a notification will be sent once the job is completed.

• Complex density map

  The assembly density map in MRC format.

• Resolution

  The resolution of the assembly density map in angstroms.

• Voxel spacing

  The dimension of a single voxel.

• Contour level

  Consider voxels with density values above the threshold.

• X, Y, and Z origins

  Optional parameters for x, y, and z origins. If not given, origins are set to 0, 0, 0.

• symmetry mode

  Select if the complex is cyclic symmetric or non symmetric. Symmetry is used in the sampling procedure for cyclic symmetric structures.

• Symmetry order

  The symmetry order of the ring (3 for trimer, 4 for tetramer etc.).

• Subunit coordinate file

  Upload coordinate file of the subunit in PDB format.

• Reset button

  Reset all the input fields.

Output

The output is a set of models that best fit the density map.

The first top 20 models are displayed as a table ranked from top-left to bottom-right and the complete list of models is found in the transformations output file (multifit.output).

Top 20 models

MultiFit.output file

This output file reports MultiFit assembly modeling solutions. Each line of 11 fields defined a single model. The solutions are sorted by fitting scores.

• Solution index

  The index of the solution.

• Solution filename

  Filename of the solution

• Fit rotation

  The rotation part (in quaternions) of a transformation found by a fiiting procedure.

• Fit translation

  The translation part of a transformation found by a fiiting procedure.

• Match size

  If anchor points matching is used, this field stores the size of the match.

• Match average distance

  If anchor points matching is used, this field stores the RMSD between the model anchor points and the density anchor points.

• Match cluster size

  If anchor points matching is used, this field stores the size of the cluster of matching anchor points.

• Fitting score

  The fitting score is defined as 1 - cross correlation score. The cross correlation (CC) score is defined as:
   , where represents all voxels in the density grid that are within two times the map resolution from any of the atoms of the protein; and where the total density of P at grid point i is    . The values of the CC score range from 0 to 1, where 1 indicates a perfect fit.
  

• Dock rotation

  The rotation part (in quaternions) of a transformation found by a docking procedure.

• Dock translation

  The translation part of a transformation found by a docking procedure.

• RMSD to reference

  If a reference structure is provided (usually in debugging mode), a RMSD to the reference is reported.

Examples

For symmetry example in building a chaperon ring, set the input data as follows:

• Number of Cn Symmetry set to 7
• EM density map
• Resolution is set to 11.5
• Spacing is set to 2.7
• Density threshold is set to 0.852
• X, Y, Z origins are set to -50, -50, -50
• Subunit file