Fit

NAME

Fit - calculate structure superpositions
SYNOPSIS

Fit ( to_axes | to_first | circular | to_mean )
DESCRIPTION

Calculate a superposition of all selected molecules, using the selected atoms. The number of selected atoms of all selected molecules must be the same, otherwise an error message is issued.

If the option 'to_axes' is selected, the principal axes of the structures are aligned to the axes of the coordinate system. This is useful for obtaining a standard orientation.

If the option 'to_first' is selected, the RMSD of each structure to the first structure is minimized seperately.

If the option 'circular' is selected, the sum of the RMSDs from the first to the second, from the second to the third, ... and from the last to the first structure is minimized.

If the option 'to_mean' is selected, the sum of all RMSDs to the resulting mean structure is minimized.

The options 'circular' and 'to_mean' use a less efficient algorithm than 'to_first', they can take very long to calculate. Their use is therefore generally not recommended. They can help in rare cases where the algorithm used in 'to_first' is numerically unstable.

At least one molecule has to be selected for 'to_axes', at least two for all other options.

For only two selected molecules, all algorithms give the same result.

This command supports groups.

EXAMPLE

Fit to_first
SEE ALSO

SelectAtom, Group, PropMol

DATE

960317


Reto Koradi, kor@mol.biol.ethz.ch