Major changes in Releases 5 and 6

The last generally released academic version of MODELLER was version 4. MODELLER 5 has not been generally released. The current version is MODELLER 6.

The major changes relative to version 4 include (this is a very incomplete list):

• New TOP loop modeling routine 'loop' significantly improves the accuracy of loop modeling (Section 3.3). It can also be used in modeling of sidechains or other parts of the structure.

• Several new statistical atomic distance-dependent potentials can typically be used for loop modeling and model evaluation.

• The ENERGY OUTPUT = 'ENERGY_PROFILE' allows construction of energy profiles for model evaluation, based on any combination of MODELLER energy terms. It replaces the ENERGY_PROFILE command.

• New functional form and parameters for the binormal $\Phi, \Psi$ restraints improve their numerical stability and accuracy.

• New TOP command SEGMENT_MATCHING facilitates exploring many different alignments in the difficult comparative modeling cases.

• New dynamic memory allocation makes MODELLER more memory efficient.

• Many bug fixes.

• Many new arguments, changed naming/meaning of arguments, and several new commands.

• Conversion from Fortran 77 to Fortran 90 was the main culprit for a very long delay before the latest release.