DialRmsd

DialRmsd - switch RMSD dialog on and off

DialRmsd ( off | on ) [ expr ]

Switch RMSD dialog on and off. The RMSD dialog is a convenient interface to the commands Fit and CalcRmsd, especially for comparisons of different molecules.

The optional second argument gives the number of groups of molecules for which residue ranges can be selected in the dialog. The default is the number of different molecules loaded.

The top two parts of the dialog allow selection of the two properties for which the global RMSDs are calculated. The common choices 'bb' (backbone) and 'heavy' (all heavy atoms) can be selected directly. A different property can be selected by chosing the 'other' button, and entering the name of the property in the corresponding text field on the right hand side. If 'other' is selected, and the text field is left empty, no global RMSDs will be calculated.

The third part of the dialog is for entering residue ranges used for superposition. Different ranges can be used for different sets of molecules given by the range in the left side text field, this is useful for comparing different molecules. Both molecule ranges and residue ranges are given in the short selection syntax, e. g. 3-10,15,18-23. The number of lines for molecule ranges is chosen when opening the dialog, and can only be changed by closing the dialog and opening it again.

The check boxes in the fourth part of the dialog select the properties that global displacements, local RMSDs, and local displacements are calculated for.

The check boxes at the bottom of the dialog select some options. The first one has to be activated when a fit with segments in a different order than their residue numbering is desired, see the Fit help page for more details. The remaining options are used for RMSD calculation. They select whether each pair of molecules is fitted before calculating the RMSDs, whether local RMSDs and displacements should be reported relative to the mean structure or as average pairwise values, and whether RMSDs between groups of molecules (as defined by the molecule ranges in the third part of the dialog) should be calculated.

The buttons at the bottom right activate the Fit or CalcRmsd command with the selected options.

The OK button closes the dialog, the Help button shows this help page.

EXAMPLE

DialRmsd on

Fit, CalcRmsd

DATE

980409