New Features

Significantly easier and more powerful superposition of molecules, proteins, nucleic acids, and membranes including ability to superimpose by MCS [ 2018-4 ]
Expanded biopolymer building capability including DNA/RNA and unnatural amino acids [ 2018-4 ]
Easily select protein atoms by secondary structure [ 2018-4 ]
Finer control over how non-bonded interaction sets are defined. Supports multiple sets of interacting atoms and restriction to within the same entry or project group [ 2018-4 ]
Calculate and display moments of inertia [ 2018-4 ]
Simultaneously extract structures of multiple PDB codes from the RCSB PDB database [ 2018-4 ]
Calculation of relative energies in the project table [ 2018-4 ]
Define default color scheme for surfaces in preferences panel [ 2018-4 ]
Improved rotation of substituents when performing ring conformation change [ 2018-4 ]
Non-bonded interaction definitions saved on a per-project basis [ 2018-4 ]
Faster minimization due to less stringent convergence criteria [ 2018-4 ]
New red-blue color ramp in color schemes [ 2018-4 ]
Indicator for excluding Non-polar H in selections [ 2018-4 ]

Support proline residue mutations in protein-protein binding, ligand selectivity, and protein stability experiments [ 2018-4 ]
Apply tautomeric state correction for ligands with multiple possible protonation/tautomeric states via pka_tautomer_correction.py [ 2018-4 ]
Generate a Map for a subset of selected nodes [ 2018-4 ]
Recognize and flag common Map issues with new "Map Issues" feature [ 2018-4 ]
Upload FMP file to LD [ 2018-4 ]
Export representative structures in the Export menu [ 2018-4 ]
Swap out the receptors in the FMP [ 2018-4 ]

Protein FEP

Generate Simulation Interactions Diagram (SID) reports from the command line [ 2018-4 ]

Generate ligand alignments ideal for FEP+ by MCS docking across one or more reference ligands in one or more protein structures [ 2018-4 ]

Mask features when creating pharmacophore hypotheses [ 2018-4 ]
Use strings, integers or reals to define active/inactive ligands for common pharmacophore perception [ 2018-4 ]

Jaguar now has the wB97X-D density functional with first and second analytic derivatives [ 2018-4 ]
The PCM implicit solvation model has been implemented in parallel [ 2018-4 ]
Jaguar input keywords are now always mirrored in the *.out file by default [ 2018-4 ]
Jaguar results script now outputs all types of polarizabilities [ 2018-4 ]
Jaguar results script now prints lambda max [ 2018-4 ]
Jaguar results script now prints the energy of the excited state [ 2018-4 ]