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Command: modeller

modeller  comparative  sequence-spec  [ sequence-spec2  ... ] [ licenseKey  key ]  other-options

modeller  scores  model-spec  [ block  true | false ] [ licenseKey  key ] [ refresh  true | false ]

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:

  1. At least one template structure.

  2. A sequence alignment that includes the sequence of the target; other sequences may also be included. The sequence alignment and template structure(s) should be open in ChimeraX and the template(s) associated with sequence(s) in the alignment.

  3. A Modeller license key specified with the licenseKey command option or entered in the Modeler Comparative dialog (this only has to be done once; the key is saved in the preferences).

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. For an example of modeling a heterodimer, see the ChimeraX Modeller highlight.

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.

Comparative Modeling Options

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.
numModels  N
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.
licenseKey  key
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.

Evaluation Server Options

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.

UCSF Resource for Biocomputing, Visualization, and Informatics / August 2020