Download MODELLER A Program for Protein Structure

Chapter 3
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.
Filename
model.top
full homol.top
loop.top
defs.top
align strs seq.top
getnames.top
homcsr.top
spline.top
cispeptide.top
default patches.top
special.top
generate model.top
single model.top
multiple models.top
refine.top
loop.top
principal.top
cluster.top
spline. top
asgl mod.top
complete.top
fit.top
mod.top
Description
the main script for comparative modeling with user alignment
the main script for comparative modeling with automatic alignment
loop modeling
variable definitions for modeling by model
aligning many structures with a sequence
generating default filenames from protein codes
generating homology-derived restraints
generating splined restraints
defining cis-peptides
making topology patches during modeling by model
generating and reading special restraints/patches for modeling by model
generating initial models for modeling by model
used by model to generate a single model
used by model to generate an ensemble of models
molecular dynamics refinement for modeling by model
modeling of loops
principal components clustering
optimization by ’clustering’ and refinement
spline most restraint types in memory
plotting for clustering analysis (requires Asgl)
generating missing atoms in a PDB file
superposing two structures, given an alignment
the main include file including all other *.top files
Table 3.1: List of Modeller scripts.
3.1
Flowchart of comparative modeling by Modeller
This section describes a flowchart of comparative modeling by Modeller, as implemented in the ’model’ Top
script. This script is also called by Quanta and InsightII. It can be used for a variety of modeling tasks, not
only for comparative modeling.
Input: script file, alignment file, PDB file(s) for template(s).
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