Comparative Models from ModBase

Models of a protein can be fetched by SwissProt, TrEMBL, GenPept or PIR accession code from ModBase using Fetch by ID or the command open (with prefix modbase:). The database contains comparative models created with Modeller, as described in:

ModBase, a database of annotated comparative protein structure models, and associated resources. Pieper U, Webb BM, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74.
When multiple modeled structures are available for the sequence, they will be opened as submodels of a single model number. The Modeller error profile (of which higher values imply lower reliability) is contained in the input file column normally used for B-factors, so it is automatically read as the attribute bfactor. Information associated with each model is shown in a dialog, or Model List.

The models are not oriented consistently, so it may be helpful to superimpose any that overlap in sequence range. Model starting and ending residue numbers are reported as Target Begin and Target End in the Model List. The command match can be used with specified residue ranges. Alternatively, MatchMaker (or its command equivalent, mmaker) can be used: it does not require specifying residue numbers, but is not as fast as match.

See also: Chimera interface to Modeller

Comparative Model List

Each row in the dialog describes a model protein structure. Besides models from ModBase, this Model List dialog is also used to show the results of running Modeller from Chimera. Each type of information [details at ModBase] can be shown or hidden using the Columns menu. Not all values are available for all models. The Model List is included in saved sessions.

The Fetch Scores menu allows using the SaliLab Model Evaluation Server to fill in certain scores for any models lacking them: zDOPE, Estimated RMSD, and Estimated Overlap (3.5 Å). The evaluation server requires a Modeller license key, provided upon free registration to academic users.

Column display settings are saved in the preferences file and used for subsequently retrieved ModBase data. If the model list is hidden or obscured by other windows, it can be raised using its instance in the Tools menu.

The model list can be sorted by the values in any displayed column by clicking the column header. Clicking the header once sorts the entries in order of increasing value and places an up arrowhead (triangle) in the header. Clicking again sorts the entries in decreasing order and places a down arrowhead (inverted triangle) in the header.

A model can be chosen by clicking on its line, and multiple models can be chosen at once. Chosen lines are highlighted in the dialog. Ctrl-click toggles the status of a line, while clicking on the first (or last) line of a contiguous block and then Shift-clicking on the last (or first) chooses all of the lines in the block.

Clicking the black arrowhead reveals/hides options for the Treatment of Chosen Models:

Option settings are saved in the preferences file and used for subsequently retrieved ModBase data.

Hide hides the dialog without removing it; Quit removes the dialog and closes the structures. Help brings up this manual page in a browser window.

UCSF Computer Graphics Laboratory / April 2014