File archive

This page contains example Python scripts for MODELLER. To submit your own examples, simply edit this page to add them.

(For large inputs, it may be easier to link to a .tar.gz or .zip file containing them. This Wiki does not allow you to upload such files, so in this case, email them to Modeller Caretaker to first have them added to the website.)

Examples

• Restraints on pseudo atoms: demonstrates the use of restraints between real and pseudo atoms.
• Mutate model: demonstrates the mutation and optimization of a single residue (SNP).
• Missing residues: demonstrates using Modeller to fill in missing residues.
• Rebuilding sequence databases: scripts to rebuild sequence databases from PDB.
• Cyclic protein: demonstrates how to build a model of a cyclic protein.
• Cluster PDBs: make a clustered representative from a set of PDBs of the same sequence.
• Using non-standard parameter files: using customized restyp.lib, par.lib and top.lib files with automodel.
• Make alpha helix: make an alpha-helical model from primary sequence alone.