Introduction

Access to the Superpose application is from the Application menu. There are three different methods for superposing models which are chosen from the box at the top of the Superpose window:
SMM - automatic secondary structure matching to superpose the equivalent SSEs of proteins
Match Close Residues - will find equivalent atoms of a roughly superposed structure; this is useful to fine tune superposition of a region of structure such as an active site
User defined matches - the user must specify the matching atoms or residues - this method includes an algorithm to find a best match of similar ligands.
These methods are explained in the folllowing sections.

In the second box down in this window is a choice of the Fixed model and a highlighted Moving model. All other models will be superposed on the fixed model. All graphical display of matches, distances and selections are shown for the fixed model and the one highlighted moving model.

In the Display of matches box are options controlling what is displayed in the main graphics window. The displayed features are always for the fixed model and the highlighted moving model. If Show matches is checked the matched atoms are shown by dashed lines and optionally labelled with the inter-atomic distances. If Highlight selected atoms is checked and a limited set of atoms has been selected for superposition then these are indicated by coloured 'pyramids' on the selected atoms.

Secondary Structure (SSM)

This method will superpose protein structures very quickly and without needing any input from the user to specify equivalent residues. The method works equally well for close homologs or for matching limited regions of similarity in very different structures. The Selection tool can be used to select limited regions of the loaded models for matching but note that the method works by first matching equivalent secondary structure elements so is not applicable to very small fragments of protein or non-protein which do not include a α-helix or β-strand. If the user's selected atoms include one Cα from a SSE then the whole of the SSE will be used in the superposition.

For some structures there may be several possible superpositions which score similarly so the Show match tool can be used to view other possible superpositions.

Match close residues

This method is useful for performing locally optimised superposition after a global superposition by SSM. For example this method will optimise the superposition of the residues forming the binding site of a ligand. To do this you need to select the required local region of the 'fixed' model. This is probably best done using the Neighbourhood of.. option from the 'fixed' model's Selection tool and selecting the Neighbourhood of the ligand. It is not necessary to make any atom selection for the 'moving' models.

This method will attempt to find the equivalent residues in the 'moving' model to the selected residues in the 'fixed' model. The criteria for equivalent residues is that the Cα atoms are within a given cutoff distance and the residues have similar orientation. The equivalent atoms within the equivalent residues must have the same name and be within a given cutoff distance. A least squares fit of all equivalent atoms is performed.

User defined matches

For this method the user has several means of specifying equivalent atoms, residues or ranges of residues to superpose. Monomers (i.e. not amino acid or nucleic acid) can be matched and the equivalent atoms will be found even if the monomers are not identical.

For this superposition method the Superposition interface is significantly changed to show a User defined matches frame

You must select two models to work on at any one time: a Fixed model and Moving model. Selecting the matching atoms or residues can be done via the User defined matches frame or via tools on the popup menu that appears if you click on an atom in the fixed or moving molecule with the right mouse button.

The User defined matches frame contains a list of the matches between the fixed and moving model and some push button commands to the right of the list. There is a tool to enter or edit matches below the list. The buttons are
Create new match will clear the match edit tool for you to enter a new match.
Copy matches from if you have already set up matches for a different pair of fixed and moving models then this tool will enable you to copy the same matches o use for the current pair of models. But note that in the User defined matches options further down the window the option to apply the superpose to all active models may also serve your purpose.
Delete selected match will delete the match curently seelcted in the list of matches
Delete selected match will delete all matches
Delete incomplete matches will delete any matches that have not been fully specified with selections for both fixed and moving model

Transforming Coordinates

You can enter a transformation matrix or move the model manually: from the model icon menu select Transform coordinates and then choose one of the options..

Move model

The model is made the 'active' moving object which is indicated by a red cross on the left of the display table. To move the model you should hold down the X key and use either the left mouse button to rotate or the middle mouse button to translate the model.

Enter transformation

In the window you can see the rotation matrix and translation vector that are currently applied to the coordinates and can reset these before clicking the Apply button to apply the transformation. Beware that you may need to click the Undo transformation button to undo any existing transformation. The program checks that your input has the correct number of elements and that the rotation matrix has a determinant of one.

Undo transform

This will return the model to its initial position.

Saving the transformed coordinates

The model will remain in the transformed position until the transformation is undone but the new coordinates will not be saved to file unless you explicitly do so. The transformation will be saved between program sessions and in status files and will be reapplied when the model is loaded. The new coordinates can be saved to file by selecting the File save/restore option from the model icon menu.

Methodology