View Modeling Settings Dialog Box

View Modeling Settings Dialog Box Features

• Modeling Method tab
  • Knowledge-based option
    • Models to build text box
  • Energy-based option
    • Apply proximity constraints within Reference option
    • Pick option
• Other Options tab
  • Keep residue numbers from template option
  • Minimize all non-template residues option
  • Preserve rotamers option
  • Optimize side chains option
  • Limit insertions to N residues option
  • Close options
• Reset button

Modeling Method tab

Choose the modeling method and make settings for the method. The choice determines the options displayed in the lower part of the panel.

Knowledge-based option

Construct insertions and close gaps using segments from known structures. With this option, you can choose to return multiple models of the structure. By default, only one is returned. The models are approximately ordered by the sequence identity and the incidence of clashes in the structure. This method is the faster method, but does not allow the use of constraints.

Models to build text box

Specify the number of models to build.

Energy-based option

Construct and refine residues that do not come from the template based on the energy, including building through structural discontinuities and optimizing side chains. This method allows constraints, both between residues in the target and between the target and ligands.

Apply proximity constraints within Reference option

Constrain selected pairs of residues to be close to each other in the final model. At least one of the residues must be in a loop, since helices and strands do not have the flexibility to adjust to the constraint. A harmonic constraint is added for the terminal heavy atoms of the side chains. If you specify a pair of CYS residues, a disulfide bond is formed.

Pick option

Click this button to pick pairs of residues in the target (reference) sequence that you want to be close to each other in the model. An annotation row opens under the sequence, and the pairs of residues are joined by green lines in this annotation. To clear all the constraints, click Clear Constraints. To clear a single constraint, pick the residue pair again.

Other Options tab

Specify other options for modeling.

Keep residue numbers from template option

Number the residues in the built structure the same as in the template, as far as possible. When using multiple templates for a single chain, the residue numbers are taken from the first template. Sequential numbering from 1 is used if the attempt to use template numbering fails.

Minimize all non-template residues option

If side chains are optimized, also optimize the residues whose structure is not derived from any of the templates.

Preserve rotamers option

Retain the rotamers for the side chains of conserved residues. These side chains will not be optimized.

Optimize side chains option

Optimize side chains, except for those attached to conserved residues if Preserve rotamers is selected.

Limit insertions to N residues option

If there is an insertion in the target (a template gap) that requires the building of a loop, build the loop if it doesn't have more than the specified number of residues, otherwise cut the target sequence and cap it with NMA and ACE. When the template that spans the insertion is cut to build the query, the template residue on the high side of the cut (higher residue number) is also deleted, so that the capping does not result in steric clashes. Cutting could be useful where there are long insertions that are not in the region of interest. The template chain retains its name, regardless of the cuts. If this option is not selected, all loops are built.

Close options

Close up discontinuities at template junctions and deletions.

• Template junctions—If there is a junction between two templates, close it if this option is selected, otherwise cap the ends of the two pieces with NMA and ACE.

• Deletions—If there are deletions in the target, join the pieces of the template when building the structure if this option is selected, otherwise cap the ends of the two pieces with NMA and ACE.

Reset button

Reset the panel to its default settings.