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:

U. Pieper, N. Eswar, F.P. Davis, H. Braberg, M.S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B.M. Webb, D. Eramian, M.Y. Shen, L. Kelly, F. Melo, and A. Sali, "MODBASE: a database of annotated comparative protein structure models and associated resources" Nucleic Acids Res 34:D291 (2006).

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.

ModBase Model List

Each row in the dialog describes a model protein structure. Each type of information [details at ModBase] can be shown or hidden using the Columns menu:

Model - model ID number in Chimera
Model Score - model reliability derived from statistical potentials (model score ≥ 0.7 indicates ≥ 95% probability of correct fold); automatically assigned as a model attribute named modbaseModelScore
Sequence Identity - percent sequence identity between target and template reported by template search; automatically assigned as a model attribute named modbaseSequenceIdentity
E-value - significance of target-template sequence alignment from PSI-BLAST template search (not the modeling alignment); automatically assigned as a model attribute named modbaseEvalue
Template PDB - PDB ID of template structure
Template Chain - chain ID of template structure
Template Begin - starting residue of region used as template
Template End - ending residue of region used as template
Target Length - length of target sequence (not model)
Target Begin - starting residue of model
Target End - ending residue of model
ModPipe Run - ModBase dataset
ModPipe Model Id - database identifier for model
ModPipe Alignment Id - database identifier for sequence alignment
Program - ModPipe version
Experiment Type - THEORETICAL MODEL
Method - HOMOLOGY MODELING

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 model 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:

Select atoms - select all atoms in the models
Choose in Model Panel - also choose the models in the Model Panel for further operations, such as:
- match... open the MatchMaker tool to superimpose structures. Of course, only models that overlap in sequence range are expected to superimpose. Model start and end residue numbers are reported as Target Begin and Target End in the model list.
- focus - center the display on the chosen model(s)
- rainbow... color the chosen model(s) over a range with the Rainbow tool
- render/sel by attr... open the Render/Select by Attribute tool, for example to color by bfactor (actually the MODELLER error profile in these models) or to show modbaseModelScore with worm thickness
- show only - show the chosen model(s) and hide all of the others
- write PDB - bring up a dialog for saving models as PDB files
In most further dialogs opened from the Model Panel, the same models will be chosen automatically.
Hide others - hide the other models in the model list

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 / May 2008