Compare/Fit Introduction

What does the Compare/Fit menu item do?

The Compare/Fit menu item allows you to compare two objects geometrically and/or functionally by aligning features in one object with a similar set of features in another object. For example, you can determine how closely three atoms in one compound can be aligned with three atoms in a second compound or determine how well atoms in a molecule match corresponding features in a hypothesis, including whether the compound meets specified topology, angle, torsion, and chemical-function constraints.

Additionally, for hypotheses that have weights assigned to their features, Catalyst can do a more complicated fit operation with a molecule. (Weights can be set automatically when generating a hypothesis or manually in the View Hypothesis workbench.) Fitting is a geometric comparison that allows certain features to have greater importance than others by assigning higher weights to them. The fit value then considers how well each feature with a weight is matched.

Whether a compare or a fit operation is performed is determined by the characteristics of the two objects selected. You can compare and fit two objects in Catalyst as follows:

Two compounds. Compare/Fit performs a geometric alignment of selected atoms in the two compounds. Can be performed in View Compound and View Hypothesis workbenches.
A compound and a hypothesis. For a hypothesis with feature weights, Compare/Fit checks that geometric constraints are met and then performs a weighted geometric fit of matching features. For a hypothesis without feature weights, it performs a geometric alignment of selected features in the two objects. Can be performed in View Hypothesis and Generate Hypothesis workbenches.
Two hypotheses. Compare/Fit performs a geometric alignment of matching functions with location constraints. Can be performed in View Hypothesis and Generate Hypothesis workbenches.

Compare/Fit provides a set of alignments between pairs of similar features of the two objects being compared. If a compound is part of a Fast Fit set of conformers, the Compare/Fit function checks each conformer for the optimum fit. If a compound is part of a Best Fit set of conformers, the Compare/Fit function manipulates all conformers within a specified energy threshold to minimize the distances between hypothesis features and mapped atoms in the molecule, or between tethered atoms in the two molecules when comparing two compounds. The result of using Compare/Fit is a set of mappings, where each mapping represents a different correspondence of atoms or features. For each mapping involving a compound, the optimum set of conformer alignments for that mapping is also presented.

More information:

Multiple mapping combinations

When two objects are compared with Compare/Fit, there may be many more mappings than expected because of the symmetry of one or both objects. For example, performing Compare/Fit on a benzene ring with a benzene ring hypothesis produces twelve mappings, since each carbon in the ring can be mapped two ways with every carbon specification in the hypothesis -- for six mappings with the ring facing up and six mappings with the ring facing down. In addition, if an acceptor function can map to two distinct lone pairs on the same atom (such as on a carbonyl oxygen), that is considered two mappings.

For each Compare/Fit operation, up to 100 of the optimum mappings (those that have the highest fit values) are reported and available for review. Also, up to twelve of the optimum conformer alignments for each mapping are reported. When comparing a hypothesis and a compound, only mappings within 2 units of the optimum fit value are reported.

Comparing two compounds

When comparing two compounds, Compare/Fit finds the optimum conformer fit (Fast Fit) for one or both compounds. Alternatively, you can perform a Best Fit, which manipulates the first 100 conformers within a specified energy threshold to minimize the distances between corresponding atom pairs in the molecules. To do the comparison, you need to use the Tether tool in the toolbox to show the correspondence of at least one atom in one compound to an atom in the second compound. These "tethered" atoms are the only parts of the two compounds that are matched in the Compare operation. You can associate many atom pairs using the Tether tool. Typically you would specify at least three tethers. Only one mapping is possible when tethers are used.

The Compare function aligns the two conformers so as to minimize the rms displacements (root-mean-squared distances between the members of tethered-atom pairs). If only one tether is used, the rms displacement is zero, since a perfect alignment can always be found using one pair of corresponding atoms.

To compare two compounds:

Bring the two molecules to be compared into the View Compound workbench shelf by any convenient method (importing, editing, or dragging from a lab or from the Stockroom).
Make sure that a conformational model has been generated for both molecules before using Compare/Fit.
Clear the display and select the two compounds on the shelf to be compared.
Select the Tools/Compare/Fit menu item. The molecules to be compared are displayed in the 2D/3D workspaces. The Compare/Fit control panel appears, displaying the names of the selected compounds in the text boxes next to the flask symbols. The names of the edit conformer or lowest-energy conformer for each molecule appear in the Conf text boxes.
In the 2D or 3D workspace, identify one or more atoms in each compound that you want to use for aligning the two conformers. For example, suppose you want to match atom Nx in molecule A with atom Ny in molecule B. To show the correspondence of these pairs of atoms, use the Tether tool in the toolbox.
If necessary, orient molecules A and B in either 2D or 3D workspaces such that the corresponding atoms can be identified and selected.
Select atom Nx in molecule A and then extend-select atom Ny in molecule B. With this one pair of corresponding atoms selected, click the Tether tool in the toolbox.

A dotted yellow tether connection appears between the corresponding atoms in the 3D workspace.
Similary, make tethers between other pairs of corresponding atoms in the two conformers to be compared. If you make a mistake, select and erase the incorrect tether, reselect the two atoms correctly, then click the Tether tool again.
In the Compare/Fit control panel, choose either the Fast Fit or Best Fit method for each compound.
Fast Fit means finding the optimum fit among the existing conformers of the molecule without performing an energy minimization.
Best Fit means that the conformers selected (either the conformer named in the Conf text box if This Conf is chosen, or the best fit conformer, as described below) are manipulated to minimize the distances between tethered objects in the molecules, while keeping the resulting conformer energy within the Energy Limit.
Choose either the This Conf or Find Best Conf method for each compound.
This Conf means that only the conformer named in the Conf text box will be compared. By default, the edit conformer or the lowest-energy conformer is selected. If you want a different conformer to be used, do the following:
1. Before selecting Compare/Fit, clear the display and select the compound on shelf that has the conformer you want to use.
2. Select the Tools/Show Conformational Model... menu item.
3. Review the conformers in the compound's conformational model in the Show Conformational Model control panel.
4. With the conformer you want to compare displayed in the control panel, select the Add to View button.
5. Drag the other compound to be used in the comparison into the workspace.
6. In the 3D workspace select both the conformer added to the view and the second molecule.
7. Select the Tools/Compare/Fit menu item. The control panel opens with the name of the selected conformer in one Conf text box and the name of the default conformer in the other Conf text box.
8. Select the This Conf button for the selected conformer and continue with the procedure.
Find Best Conf means that all conformers in the molecule's conformational model will be examined to find the optimum fit with the selected conformers in the other compound.
If you are using Best Fit, you can set the Energy Limit threshold. This value limits the amount of extra energy that Best Fit is permitted to introduce during the comparison. The default value is taken from the energy threshold of the conformational model.
Select the Compare button in the Compare/Fit control panel. Compare finds alignments of selected conformers for each molecule so as to minimize the rms displacement between the tethered atoms and then displays the optimum mapping of the conformers in the View Compound 3D workspace.
To simplify the display, the tethers are not shown.
The RMS Displacements value is shown in the control panel for the displayed fit, and the energies of the conformers providing the optimum fit are displayed in the respective Conf Energy boxes. The energy of the first molecule's conformer is displayed in the top Conf Energy box, and the energy of the second molecule is displayed in the second Conf Energy box.
If no mapping was possible, an Alert message is displayed.
The number of mappings and conformers that meet the energy threshold limits is reported in the Mappings/Confs text box, in the form M: n / m | C: b / c, where n is the number of the mapping being displayed, m is the total number of mappings that met the criteria, b is the number of the conformer fit being displayed associated with mapping n, and c is the total number of conformer fits for that mapping. A maximum of 100 optimum mappings and 12 optimum conformer alignments are presented for any Compare operation.

For compound-compound comparisons, which require tethers, only one mapping is found.
The names of the conformers with optimum fits are displayed in the Conf text boxes. The number above the slider indicates which conformer fit is being viewed in the 3D workspace. Initially it is 1, which is the optimum fit. A summary of statistics for each Compare operation is presented in the History Window. To review it, select the Windows/History Window menu item.
To view the other conformer fits, click the Mappings/Confs button and select Confs. Conformer fits are numbered and listed in order of how well they align, as measured by their rms displacement score.
Click the Fast Forward button to step through all the conformer fits automatically. Stepping stops at the last fit on the list.
During automatic stepping through the fits, click the Stop button if you want to examine a particular conformer fit in more detail. After stopping on a conformer, you can use the Rotate function (right mouse button) to rotate both conformers together to examine how they align.
Extend-move function. To unlock the two conformers and move one conformer away from the other in order to see individual atoms or bonds more clearly, use the middle mouse button to drag one conformer away from the other conformer.
You can then restart automatically stepping through other alignments by clicking the Forward or Backward button.
To view other mappings, set the Mappings/Confs popup to Mappings and use the Forward, Reverse, and Stop buttons to control the mapping displayed in the workspace, as described above for viewing conformers.
If you used the best-fit method of Compare and new conformers were created as a result of minimization, you can use the Save Confs button to attach the new conformers to the associated compound. If you do not save the conformers, any new conformers created by minimization are deleted at the end of the Compare process. With the fast-fit method, new conformers may be created to indicate how hydrogens have shifted to align with hydrogen-bonding features.
If you want to repeat the Compare operation on the same two molecules, but with different atoms tethered, attach new tethers to the two molecules in one of the displayed alignments. You may want to select This Conf this time if you did the last Compare in Find Best Conf mode.
To see all the atoms better to attach the tethers, use the 2D workspace or use the extend-move method to unlock and separate the conformers.
When you have finished the Compare operation with these molecules, select the Cancel button. The Compare/Fit control panel is closed, but the aligned conformers remain in the workspace in case you want to compare them with another molecule.
Select the Edit/Clear Display menu item if you want to clear the workspace.

Comparing a compound and a hypothesis

The Compare/Fit function searches for the optimum set of mappings (3D alignments between features in the hypothesis and matching features in the molecule) and conformer alignments for each mapping. You can choose one of two Compare/Fit methods: use all features contained in the hypothesis to determine the mappings or restrict the mappings by using tethers (connections between corresponding features).

You also can choose a particular conformer to use in the comparison and can choose to do a fast fit or best fit of the conformational model. Best Fit manipulates the first 100 conformers within a specified energy threshold to minimize the distances between hypothesis features and mapped atoms in the molecule.

A typical Compare/Fit operation between a hypothesis and molecule produces a ranked set of geometric mappings and, for each mapping, a ranked set of conformers that matched the hypothesis. You can view the mappings and conformers individually in the 3D workspace of the workbench. For a typical successful Compare operation, a list of matched features appears in the History Window, along with a fit value and the rms displacement, if possible.

The particular type of operation performed in Compare/Fit is determined by the characteristics of the selected hypothesis. The following are the characteristics that can be included in a hypothesis, and a summary of how their presence affects a Compare/Fit operation with a compound:

Feature weights. If features in the hypothesis have weights (set with the Generate Hypothesis or Set Feature Weight menu item), a set of mappings with weighted fit values is computed. If the hypothesis does not have weights on any features, a set of geometric alignments of tethered features or matching location constraints is performed, and the minimum rms displacement values are computed.
Location constraints. Rms displacements are computed for all location constraints that are matched in the compound. If there are no location constraints, matching features are mapped and a fit value computed for each mapping, but no rms displacement can be computed.
Chemical functions (hydrogen-bond donor and acceptor, hydrogen-bond acceptor lipid, hydrophobe, positive and negative charge, and positive and negative ionizable). All combinations of features in the hypothesis and matching features in the molecule are mapped. With weights, a fit value is computed. With location constraints, a minimum rms displacement value is computed.
Chemical fragment (topology specifications). Every atom and bond specification in a hypothesis feature must be matched in the compound for the feature to be considered in a mapping or a fit.
Distance, angle, and torsion constraints. All aspects of a constraint on a feature must be met for the feature to be considered in a mapping or a fit.
Excluded volumes. Catalyst models excluded volumes as pseudoatoms (carbon atoms). Van der Waals interactions are computed between the molecule and any excluded volume, and this energy is added to the total energy of the molecule. Catalyst returns mappings whose excess energy (including the excluded-volume energy) does not exceed the value you specify for Energy Limit.
Property constraints (1D values). This type of constraint is used only in database searches (including the minimum-fit property); properties are not considered in Compare/Fit.

Compare/Fit without Tethers. Compare attempts to meet all constraints and map each function in the selected hypothesis to a matching part of the selected compound. A different mapping is generated for each combination of one or more features in the hypothesis that is matched in the compound. For each best-fit Compare/Fit operation, up to 100 different mappings are presented, ranked in order of quality based upon fit or rms displacement. In addition, for each unique mapping, up to 12 of the optimum conformer alignments are also available for review.

For some hypothesis and compound combinations, you may obtain too many mappings, many of which may be of no interest for your project. Unwanted mappings can be limited during Compare by attaching tethers between features of the hypothesis and compound.

Compare/Fit with Tethers. You can specify a correspondence between particular pairs of features in a hypothesis and a compound with the Tether tool. Attaching tethers between matching features of interest eliminates other mappings and speeds up the processes of generating the alignments and reviewing the results.

You can compare a compound with a hypothesis that you have generated in the Generate Hypothesis workbench or with one that you have built in the View Hypothesis workbench (and then processed with the Regress Hypothesis menu item). See the description of the Regress Hypothesis menu item.

To compare a compound and a hypothesis:

Unless you plan to use only the edit conformer, make sure that a conformational model has been generated for the compound, in order to find the conformers that fit the hypothesis optimally.
To check whether the compound has a conformational model, select its icon on the shelf in the Stockroom or lab. The Status Area reports either the number of conformers or "No Conf model".
If it has no conformers, see To generate conformers.
Bring the compound and hypothesis to be compared into the workbench and clear the display.
If you want to use all conformers in the compound conformational model in the comparison, select the compound and hypothesis on the shelf.
If you want to use a particular conformer in the comparison, do the following:
1. Select the compound on the shelf.
2. Select the Tools/Show Conformers menu item.
3. In the Show Conformers control panel, review the conformers in the compounds' conformational model.
4. With the conformer you want to use displayed in the control panel, select the Add to View button. The selected conformer is displayed in the 3D workspace (it may be rotated from its orientation in the control panel).
5. Drag the hypothesis to be used in Compare into the workspace with the conformer.
6. In the workspace, select both the conformer added to the view and the hypothesis.
Select the Tools/Compare/Fit menu item.
The Compare/Fit control panel opens, with the names of the hypothesis and the compound in the text boxes adjacent to the hypothesis and compound symbols. Unless you have selected a conformer to be used with Compare/Fit, the default conformer in the Conf text box is the lowest-energy conformer.
Tether Constraints. If you want Compare to evaluate all possible mappings that satisfy the constraints in the hypothesis and do not want to limit possible fits, proceed to Step 6.
If you want to constrain the number of mappings considered in the Compare process, you must identify one or more features in the hypothesis that correspond to features in the compound. You then tether one or more corresponding pairs of features to specify the alignment of the two objects. Compare tries to align the compound and hypothesis using just the tethered features and to minimize the rms length of the tethers.
For example, suppose you have a compound CompA and a hypothesis Hyp1 with a hydrogen-bond acceptor HBA1. You want function HBA1 to align only with atom Nx in CompA. To show the correspondence of this pair of features, use the Tether tool in the toolbox, as follows:
1. Orient CompA and hypothesis Hyp1 in the workspace so that their corresponding features can be identified. You can do this in the 2D or 3D workspace, whichever is more convenient.
  If you are not sure about what functions are in the compound, use the Tools/Show Function Mapping menu item in the View Hypothesis workbench.
2. Select atom Nx in CompA and extend-select function HBA1 or its location constraint in Hypo1. With the pair of corresponding features selected, click the Tether tool in the toolbox.
  A dotted yellow tether between the corresponding features appears in the 3D workspace.
3. Similarly, you can connect tethers between other pairs of corresponding features. Each pair is attached with a separate tether.
In the Compare/Fit control panel, select Fast Fit or Best Fit. Fast Fit finds the optimum conformer that fits the hypothesis. Best Fit means that the first 100 conformers are manipulated within the specified energy threshold to minimize the distances between hypothesis features and mapped atoms in the molecule.
Generally you would use the default Find Best Conf method for the compound.
Find Best Conf means that all conformers in the generated set are examined to find the optimum fit with the hypothesis. After the best-fitting conformer is found, you can select the This Conf button to do a Best Fit on the optimum-fit conformer.
You can set the Energy Limit, which limits the amount of extra energy that Best Fit is permitted to introduce during the comparison. The default value is taken from the energy threshold of the conformational model.
Select the Compare button in the Compare/Fit control panel.
Compare/Fit searches for the optimum alignments for any tethers you have attached or, with no tethers, searches for alignments that match as many features in the hypothesis as possible with the features in the compound.
If any mappings are possible, the optimum one is displayed in the workspace. Other mappings that do not fit as well are available for review in the control panel.
To simplify the display, tethers are not shown.
If a fit value can be computed, it is displayed in the Fit text box. If not, the Status Area displays N/A.
If the hypothesis can estimate activity, a value is displayed in the Estimate text box.
The energy of the conformer with the optimum fit is displayed in the Compound Conf Energy box.
If no mapping was possible, a message is displayed.
If several mappings meet the constraints, their number is shown in the Mappings/Confs text box as M: 1/n, where n is the number of mappings found and 1 indicates the first of the set.
If several conformers meet the criteria, their number is shown in the Mappings/Confs text box as C: 1/n, where n is the number of conformers that matched and 1 indicates the first of the set. Conformers are listed roughly in order of how well they align.
To view the other conformer alignments, set the Mappings/Confs popup to Confs.
Conformer fits are numbered and listed in order of how well they align, as measured by their rms displacement score.
Click the fast-forward button to automatically step through all the conformer fits. Stepping stops at the last fit on the list.
During automatic stepping through the fits, click the stop button if you want to examine a particular conformer fit in more detail.
After you use the stop button, you can use the Rotate function (right mouse button) to rotate both conformer and hypothesis together to see how they align.
Extend-move function. To unlock the conformers and hypothesis and move one object away from the other in order to see individual atoms or bonds more clearly, use the middle mouse button to drag one object away from the other.
You can then restart automatically stepping through other alignments by clicking the forward or backward button.
To view other mappings, set the Mappings/Confs popup to Mappings, then use the forward, reverse, and stop buttons to control the mapping displayed in the workspace, as described above for viewing conformers.
If you used the Best Fit method of Compare and new conformers were created as a result of minimization, you can use the Save Confs button to attach the new conformers to the associated compound. If you do not save the conformers, then any new conformers created by minimization are deleted at the end of the Compare process.
If you want to repeat the Compare operation on the same two objects, but with different tethers, attach new tethers in one of the displayed alignments. You may want to select This Conf this time, if you did the last Compare using the Find Best Conf mode.
To see all the features better to attach the tethers, use the 2D workspace or use the extend-move method to unlock and move the conformers apart, as described previously.
When you have finished doing Compare with these objects, select the Cancel button.

What rms displacements and fit value mean in Compare

Each type of Compare/Fit operation has an associated measure of the quality of the alignment to indicate how closely corresponding features or atoms can be oriented. A ranking of mappings, starting with the optimum fit, is presented for each Compare/Fit operation.

Rms displacement

In comparing two compounds or two hypotheses, the rms displacement is used to measure how well the two objects can be aligned. The rms displacement is the root-mean-square of the distances between the corresponding pairs of features for each alignment. A lower rms displacement indicates a better fit; a zero value indicates an alignment in which the corresponding features are coincident.

Weights and constraint tolerances are not involved in comparing two molecules. By default, the weights and constraint tolerances are not involved when comparing two hypotheses. However, Catalyst can be instructed to consider the differences between feature weights and/or tolerances by setting the .Catalyst parameters compare.considerWeight and compare.considerTolerance to 1. See Clustering hypotheses for an explanation of how this affects calculation of the rms displacement.

Fit Value

In comparing a compound and a hypothesis, the quality of the mapping is indicated by the fit value. A higher fit value represents a better fit; a perfect mapping of features would result in a fit value equivalent to the sum of the weights of the features in the hypothesis.

The computed fit value depends on two parameters: the weights assigned to the hypothesis features and how close the features in the molecule are to the centers of the corresponding location constraints in the hypothesis.

Weights on features indicate the importance of the feature relative to other features. If a weight is assigned to any feature, all other features in the hypothesis are assigned a default weight of 1.0. See the description of the Set Feature Weight menu item.

Fit value is computed as follows:

: Fit = sum over mapped features f of weight(f) * [ 1 - SSE(f) ]

where:
: SSE(f) = sum over location constraints c on f of ( D ( c ) / T ( c ) )²

where:
: D = the displacement of the feature from the center of the location constraint, and T = the radius of the location constraint sphere for the feature (tolerance).

The hypothesis and conformer are aligned so as to maximize the fit (minimize the weighted sum of square displacements).

If no weights are assigned to a hypothesis, no fit value can be computed, and only the rms displacement will be computed for any molecule features matching hypothesis features with location constraints.

Mappings and fit values are computed for as many combinations as possible that successfully map sets of corresponding features. For each mapping, a fit value is also computed for all conformers in the compound's conformational model.

The process of mapping hypotheses with weights to compounds involves:

Initially, constraints on mapped features, such as distance, angle, and torsion constraints, are checked to see if they are satisfied. Features that do not satisfy these absolute constraints do not participate in the mapping or contribute to the fit value.
Weights are summed for features in the hypothesis that have no location constraints but are matched in the molecule. Since they have no location constraints, they must only be present in the molecule.
Corresponding features with location constraints are aligned with each conformer in the molecule to obtain the optimum orientations and the highest fit values. The contributions for each feature are summed, considering how close to the center of the location constraint each is mapped.
The mappings and conformer fits for each mapping are ranked by fit value, and those with the highest fit values are available for review.

Some examples of fit-value computations are:

If there is a perfect mapping, meaning that every hypothesis feature has a corresponding compound feature and each feature with a location constraint is mapped in the center of the sphere, then the fit rating equals the sum of the weights in the hypothesis.
For example, if the hypothesis has two features with location constraints that each have a weight of 1.0 and each is mapped in the exact center of the corresponding compound feature, and if in addition it has one matched feature with a weight of 1.0 but without a location constraint, the fit value would be 3.0.
If the hypothesis has four features with location constraints that have weights of 0.5, 1.0, 2.0, and 3.0 and the location constraints are mapped exactly in the center, the fit value would be 6.5.
If you have the same hypothesis, molecule, and weights as in the previous example, but no location constraints, the fit value also would equal 6.5. This is because, by having no location constraints, the locations of the molecular features are not considered, so if all features are present you still have a perfect fit.
If the optimum alignment maps a feature a distance D from the center of a location constraint sphere with radius T, it decreases fit value based upon the term (D/T)², as follows:
For a feature located at the sphere perimeter, the fit is reduced by an amount equal to 100% of the weight of the feature.
For a feature located halfway between the center and the perimeter, the fit is reduced by 25% of the weight of the feature.
For a feature located at the center, the fit value is not reduced.

Location constraints and weights are automatically computed during the Generate Hypothesis operation. Location constraints and weights can be manually modified or added to constructed or generated hypotheses in the View Hypothesis workbench using the Constraints menu. See To add location constraints.

For more details about setting and using weights, see the description of the Set Feature Weight menu item.

Comparing a hypothesis and a hypothesis

When comparing two hypotheses, by default all combinations of features with location constraints on one hypothesis are compared with the same features having location constraints on the other hypothesis. All mapping combinations are presented for review. Unwanted mappings can be limited by attaching tethers between specified location constraints. Topology contained in a hypothesis must have location constraints and tethers in order to be considered by Compare.

Compare ignores features that do not have location constraints. If tethers are used for operations comparing two hypotheses, they must be connected to location constraints.

When comparing two hypotheses, each location constraint in one hypothesis is mapped to each similar type of location constraint in the other. The Compare function aligns the two hypotheses so as to minimize the rms distances between the centers of the corresponding pairs of location constraints for each mapping.

Subsets of features with location constraints are considered -- not every location constraint has to map to every other similar location constraint. The mappings are ranked first based upon the number of pairs of location constraints that match and then on the minimum rms displacement.

If you want, you can tether one or more pairs of location constraints on the hypotheses, so as to limit the number of mappings that are considered. The rms displacement is computed for the tethered features.

To compare two hypotheses:

Bring the hypotheses to compare into the workbench.
Clear the display and select the two hypotheses on the shelf.
Select the Tools/Compare/Fit menu item.
The hypotheses to be compared are displayed in the workspace.
The Compare/Fit control panel appears, displaying the names of the selected hypotheses in the text boxes next to the hypothesis symbols.
Tether Constraints. If you want Compare to evaluate all possible alignments of matching location constraints in the two hypotheses and do not want to limit possible fits, proceed to Step 5.
If you want to constrain the number of mappings considered in the Compare process, you must identify one or more functions in the two hypotheses that correspond. You then tether pairs of functions to specify the alignment of the two objects. For example, suppose you want HB Acceptor1 in hypothesis YYY to align only with HB Acceptor3 in hypothesis ZZZ. (You can tether dissimilar functions if you want them to align.) To show the correspondence of a pair of functions, use the Tether tool in the toolbox:
1. Orient hypotheses YYY and ZZZ in the 3D workspace so that the tethered features are visible and can be easily selected.
2. Select HB Acceptor1 in hypothesis YYY and extend-select HB Acceptor3 in hypothesis ZZZ.
3. With the set of corresponding functions selected, click the Tether tool in the toolbox.
  
  A yellow tether appears between the corresponding functions in the 3D workspace.
4. If desired, connect tethers between other pairs of functions that have location constraints in the two hypotheses. To align both points in a vector feature, a tether must be added to each end.
Select the Compare button in the Compare/Fit control panel.

Compare matches as many location constraints in the two hypothesis as it can, considering any tethers you have attached. The optimum mapping is displayed in the workspace, and the rms displacement is displayed in the control panel. Other mappings that do not fit as well also are available for review in the control panel.

To simplify the display, tethers are not shown.

If at least one hypothesis has weighted features, mappings of other pairs of location constraints are also generated in addition to those involving tethers. Location constraints are considered for inclusion in a mapping if they constrain corresponding atoms or points in features with the same definition and if no tethered location constraint refers to the same feature.

If several mappings meet the constraints, theis number is shown in the Mappings box as 1/n, where n is the number of mappings found.

If no mapping was possible, a message is displayed.

Examples of results of Compare/Fit operations

Here are some examples of the results of sample Compare/Fit operations:

[Top] [Index]