Molecular Topology

Before assigning a molecule one should read in the molecular topology. This is defined in a sequence file. At its simplest this is a file with the three letter (or four for nucleotides) code, one residue per line. Three and four letter codes correspond to the names of ".prf" files in the NMRViewJ residue library. There are two libraries, one with IUPAC nomenclature and one with that followed by XPLOR. Integer values can follow the residue codes to provide numbering that doesn't start at "1". Complex molecular structures can be defined with hetero and homo-multimers, peptides, DNA, and RNA mixed together. Small molecule ligands can be specified as well. Once read in, the complete topology (including small molecule components) can be stored in the STAR file. A graphical interface also allows you to enter simple topologies with the three letter or one letter codes.

Structure Analysis

Families of molecular coordinates can be read in from a single PDB file with multiple MODEL sections, or from a set of individual PDB files. If the current topology is in IUPAC nomenclature, but the PDB file is in XPLOR nomenclature, atom names will be swapped as they are read in. The structure tool displayed here can identify "core" regions of the structure, calculate superpositions using the specified residue and atom filters, and align all structures on a selected entry. In the calculate mode the "most representative" structure is identified (shown with an RMSD value of 0.0 in the table). RMSD values in the table are from each structure to that structure. The structure analysis tool is also used to activate and deactivate individual members of the family of structures. Deactivated ones will not be used in calculations involving, for example, NOE violations.

Residue RMSD Plot

A plot of the atomic RMSD on a residue basis can be displayed. This same calculation is used in the core identification tool mentioned above

Ramachandran Plot

Clicking the Rama button will generate a Ramachandran (Phi-Psi) plot of the structures. Only those structures that are activated (have a value in the state column of "1" will be used. Each model is displayed with a different color and symbol and a legend is displayed to show this symbol-model match.

Molecular Display

The molecular viewer can display one or more structures to allow you to view the family of structures.


2 August 2016: New Versions of NMRView, dataChord Spectrum Miner and Analyst, and NvFX

New Google Groups for NMRViewJ and NMRFx Processor

Our first publication on NMRFx appears at the Journal of Biomolecular NMR