The choice of base reference system is that established at the Tsukuba meeting (13 (link)). See the work of Lu and Olson (25 (link)) for a full discussion of the influence of such a choice. The graphical position of this reference system with respect to standard purines and pyrimidines can be found in the Tsukuba reference. In order to avoid having to give the reference system in Cartesian coordinates for each standard base, we calculate it using chosen base atoms. These are C1', N1(Y)/N9(R) and C2(Y)/C4(R) in standard bases (where Y is a pyrimidine and R is a purine). Users can change these atoms to deal with non-standard cases. For example to deal with the RNA base pseudouridine which is linked to the phosphodiester backbone through C5, the equivalent atoms would be C1', C5 and C4. For completeness, we provide our construction method: this involves the atoms forming the glycosidic bond between each base and the sugar-phosphate backbone, N1–C1' for pyrimidines and N9–C1' for purines and the normal to the mean plane of the base (termed bN below). The direction of the normal is given by the cross product (N1–C1') × (N1–C2) for pyrimidines and (N9–C1') × (N9–C4) for purines. The base reference point (termed bR below) is obtained by rotating a vector of length d (initially aligned with the N–C1' direction) clockwise by an angle τ1 around the normal vector passing through the N atom. The next vector of the reference system, pointing towards the phosphodiester backbone joined to the base (termed bL below) is obtained by a similar rotation, but using a unit vector and the angle τ2. The last vector of the reference system, pointing into the major groove, bD, is obtained from the cross product bL × bN. For the Tsukuba convention, τ1 = 141.47°, τ2 = −54.41° and d = 4.702 Å. The former Curves program used values of 132.19°, −54.51° and 4.503 Å, respectively. The major impact of this change is a movement of the base reference point towards the major groove, which means that Xdisp values (measuring the displacement of bases or base pairs along the pseudodyad with respect to the helical axis) become more positive by 0.77 Å with the new reference system. There is also a change in slide, which is more positive by 0.47 Å with the new reference. For comparisons with earlier results, Curves+ allows the user to optionally select the old reference system.
Since low resolution structures, and also snapshots from MD trajectories, may contain deformed bases, it is advisable to start by least-squares fitting (26 (link)) a standard base geometry to the atoms in the input structure before defining the base reference system. Curves+ provides the standard geometries for a number of DNA and RNA bases in a data file (standard_b.lib) that can be modified and extended by the user. Only ring atoms (plus the bound C1') need to be defined in each case. Using this data, Curves+ will automatically perform least-squares fits to the input data, but this fitting can be prevented by the user if desired.
Since low resolution structures, and also snapshots from MD trajectories, may contain deformed bases, it is advisable to start by least-squares fitting (26 (link)) a standard base geometry to the atoms in the input structure before defining the base reference system. Curves+ provides the standard geometries for a number of DNA and RNA bases in a data file (standard_b.lib) that can be modified and extended by the user. Only ring atoms (plus the bound C1') need to be defined in each case. Using this data, Curves+ will automatically perform least-squares fits to the input data, but this fitting can be prevented by the user if desired.
