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MODELLER scripts

This section describes some of the MODELLER scripts found in the $MODINSTALL7v7/bin/__*.top files. All these files and brief descriptions are listed in Table 3.1.


Table 3.1: List of MODELLER scripts.
Filename Description
__ model.top the main script for comparative modeling with user alignment
__ full_homol.top the main script for comparative modeling with automatic alignment
__ loop.top loop modeling
__ defs.top variable definitions for modeling by model
__ align_strs_seq.top aligning many structures with a sequence
__ getnames.top generating default filenames from protein codes
__ homcsr.top generating homology-derived restraints
__ spline.top generating splined restraints
__ cispeptide.top defining cis-peptides
__ default_patches.top making topology patches during modeling by model
__ special.top generating and reading special restraints/patches for modeling by model
__ generate_model.top generating initial models for modeling by model
__ single_model.top used by model to generate a single model
__ multiple_models.top used by model to generate an ensemble of models
__ refine.top molecular dynamics refinement for modeling by model
__ loop.top modeling of loops
__ principal.top principal components clustering
__ cluster.top optimization by 'clustering' and refinement
__ spline. top spline most restraint types in memory
__ asgl_mod.top plotting for clustering analysis (requires ASGL)
__ complete.top generating missing atoms in a PDB file
__ fit.top superposing two structures, given an alignment
__ mod.top the main include file including all other __*.top files




Subsections
next up previous contents index
Next: Flowchart of comparative modeling Up: MODELLER A Program for Previous: DEBUG_FUNCTION test   Contents   Index
Ben Webb 2004-10-04