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