Nucleotide numbers within one strand can be given as a list e.g. 1 2 3 4 ...
Consecutive numbers from M to N can be given using the bracket notation M:N
Bracket and list notations can be mixed within one strand
Bases not to be used for calculating the helical axis are indicated by a negative sign
Missing nucleotides/bases are indicated by a zero
Paired bases must appear in equivalent positions in each strand
Base numbers used by Curves+ refer to their order of appearance in the input PDB file
(and not their PDB unit numbers) and note that anything other than nucleic acids is ignored
e.g. in 1KX5.pdb (a nucleosome) the last two chains in the PDB file (I,J) are the DNA, the unit
numbers in each strand are -73 to +73, but the Curves+ input is 1:147 for the first strand (5’-3’)
and 294:148 for the second strand (3’-5’). Note base 1 is paired to base 294, 2 to 293, etc.
Curves+ parameters:
| Fit: | if T standard base conformations are fitted to the I/P coordinates (recommended) |
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| Circ: | set T to analyze circular DNA |
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| Line: | set T to find optimal linear helical axis (not compatible with Zaxe=T) |
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| Zaxe: | set T to use Cartesian Z-axis as helical axis (not compatible with Line=T) |
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| Refo: | set T to use old base reference system (pre-Tsukuba convention) |
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| Back: | atom used to define backbone splines (default P, can be any backbone atom) |
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| Wback: | width of backbone (default 2.9 - used in calculating groove width, depends on ‘Back’) |
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| Wbase: | ½ width of base pair (default 3.5 - used in calculating groove depth) |
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| Naxlim: | if naxlim > 0, calculates overall bend skipping naxlim base levels at the 5'- and 3'-ends (default 0) |
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| RVFac: | factor multiplying the length of the radial vectors indicating curvature in the _R.pdb graphical ouput file (default 7.5) |
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Other parameters:
| 3D Viewer: | Select from the following options the 3D viewer to be used in the results page:
- JSmol:
- Full-featured molecular graphics environment using HTML5 canvas. Right-click in the viewer to visualise the feature menu. See also http://www.jmol.org/.
- NGL (default):
- Fast molecular viewer using WebGL. This viewer is very fast to load and run, and is recommended for large molecules or complexes. See also the NGL github page.
- None:
- No molecular viewer will be used in the results page: plots and output files will still be available.
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