MODELLER commands

Sections in this Chapter describe technical aspects of MODELLER. They include:

• miscellaneous rules and features of MODELLER (Section 2.1);

• dealing with stereochemical parameters and molecular topology (Section 2.2);

• handling of atomic coordinates (Section 2.3);

• comparing and searching of sequences and structures (Section 2.4);

• calculating spatial restraints (Section 2.5),

• deriving the model by minimizing the restraints (Section 2.6).