The modeller comparative command performs comparative or “homology” modeling of proteins by running Modeller on a web service hosted by the UCSF RBVI. It is the command-line implementation of the Modeler Comparative tool. Additional scores for the resulting models can be obtained from the SaliLab Model Evaluation Server using the Modeller Results dialog or the modeller scores command. (Any atomic model can be “evaluated” with this command, but in the absence of a Modeller Results dialog to show the scores, the only result will be to assign them as model attributes.)
Modeller is developed by the Šali Lab, and its 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.
Modeller comparative modeling requires the following for each target chain:
The target sequence can be fetched from UniProt or opened from a file. That single sequence suffices as the “alignment” if the template is similar enough in sequence to associate with it (see example). Alternatively, a multiple sequence alignment of the target and template(s) can be opened from a file, if available, or obtained by using the blastprotein command to search for templates with the target sequence as a query.
With the above requirements in place, the only mandatory command argument per target is the sequence-spec. For example, the following command specifies the next-to-last sequence in the alignment super8.msf as the target:
modeller comp super8.msf:-2 multichain true num 3 het true
Templates are not specified in the command. All of the structure chains associated with any sequence in the same alignment as the target will be used as templates.
When results are returned, the new models are opened, listed in the Model Panel along with any other models present in ChimeraX, and automatically superimposed on the lowest-model-ID template structure with matchmaker. Scores for the comparative models are shown in a Modeller Results panel.
multichain true | false
Whether to retain template homomultimeric states (default true); for example, if the template structure is a homotrimer, whether to model the target as a homotrimer instead of as a monomer with three templates.
Number of models to create (default 5, maximum 1000).
fast true | false
Whether to use fast/approximate mode (~3 times faster) to get a rough idea of model appearance or to confirm that the alignment is reasonable (default false). This mode does not randomize the starting structure (generates only a single model) and performs very little optimization of the target function.
hetPreserve true | false
Whether to include HETATM residues other than water (ligands, ions, detergent, etc.) from templates in the output models (default false). Any such residues not desired in the output should be deleted from the template(s) beforehand if the option is turned on.
waterPreserve true | false
whether to include water residues from templates in the output models (default false). Any water residues not desired in the output should be deleted from the template(s) beforehand if the option is turned on.
hydrogens true | false
Whether to include hydrogen atoms in the output models (default false); increases computation time by approximately a factor of 4.
block true | false
Whether to wait for the calculation to finish before starting to execute any subsequent commands, default true when the modeller command is being executed in a command script and/or in nogui mode, otherwise false.
Use of Modeller requires a license key, but it only has to be specified once in ChimeraX; the key is saved in the preferences. Academic users can register free of charge to receive a license key. Commercial entities and government research labs, please see Modeller licensing.
refresh true | false
The refresh option applies to modeller scores only and specifies whether to overwrite existing scores (default false, do not overwrite existing scores). Refreshing scores may be useful after models have been modified (for example, to delete untemplated regions built as extended tails). However, since re-evaluation does not use all of the same information as does scoring during the original modeling process, it may worsen pre-existing GA341 and zDOPE scores and should only be used after making modifications that are expected to improve the scores.