Chimera Interface to Modeller

Chimera provides a graphical interface to running the program Modeller, either locally or via a web service hosted by the UCSF RBVI. Two types of calculations are available:

Modeller is developed by the Sali Lab. Use of Modeller, whether a previously downloaded copy or via web service, requires a license key. Academic users can register free of charge to receive a license key. (Commercial entities and government research labs, please see Modeller licensing.) Modeller users should cite:
Comparative protein modelling by satisfaction of spatial restraints. Šali A, Blundell TL. J Mol Biol. 1993 Dec 5;234(3):779-815.
See also: Build Structure, Rotamers, Multalign Viewer, mda, ModBase fetch, modifying and saving data, the Comparative Modeling tutorial

Comparative Modeling with Modeller

Comparative modeling requires a structure to serve as a template, and a target-template sequence alignment. There are several ways to obtain these inputs using Chimera. Sequence alignments are shown in Multalign Viewer. The Chimera interface to comparative modeling with Modeller can be started by choosing Structure... Modeller (homology) from the Multalign Viewer menu, or called with mda. With this interface, *only a single chain or subunit can be modeled at a time.* Modeling a multimer or complex requires running Modeller outside of Chimera.

OK starts the calculation and dismisses the panel, while Apply starts the calculation without dismissing the panel. Close dismisses the panel without performing any calculation. Help brings up this manual page in a browser window.

Running Modeller is a background task. Clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired.

After the calculation has finished, the comparative models are opened in Chimera and can be saved in the usual ways. The models are automatically superimposed onto the template (or the lowest-numbered of multiple templates) using matchmaker defaults, and the view is focused on that template. The models are associated with the target sequence, and the RMSD header displayed in the sequence window. Model scores are shown in a Model List, the same dialog used for comparative models fetched from ModBase. Loops or other parts of a model can be subjected to further refinement.

Running Modeller with identical inputs on different machines may give different (but equally valid) results, due to small numerical differences that can lead to finding different local optima of the modeling objective function.

Building/Refinement with Modeller (Model/Refine Loops Model/Refine Loops icon )

The only required input for Modeller building or refinement is a protein structure. Missing segments can be built de novo, or existing segments refined by generating additional possible conformations. Building and refinement can be applied to protein structures regardless of whether they were modeled or determined experimentally.

The Chimera interface to Modeller for building or refinement can be accessed by starting Model/Refine Loops, a tool in the Structure Editing category, or by choosing Structure... Modeller (loops/refinement) from the Multalign Viewer (Sequence tool) menu. Using Model/Refine Loops is equivalent to using the Sequence tool to show the sequence of a chain, then using its menu to show the interface. If the structure chain is associated with a sequence in an alignment in Multalign Viewer, however, the alignment sequence can be used instead of the individual sequence.

OK starts the calculation and dismisses the panel, while Apply starts the calculation without dismissing the panel. Close dismisses the panel without performing any calculation. Help brings up this manual page in a browser window.

Running Modeller is a background task. Clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired.

After the calculation has finished, the models (each including the unchanged parts of the protein in addition to what was built or refined) are opened in Chimera and can be saved in the usual ways. The models are associated with the sequence, and the RMSD header displayed in the sequence window. Model scores are shown in a Model List, the same dialog used for comparative models fetched from ModBase.


UCSF Computer Graphics Laboratory / July 2015