This tool calculates the pseudorotational phase angle and puckering amplitude for nucleosides/nucleotides.

File Submission Form
Input File

(All major file formats, including PDB, SDF, MOL, XYZ ..., are supported. The file may contain one molecule, several molecules, a DNA/RNA oligonucleotide or DNA/RNA complexed with a protein.)
Type of Structure
Molecule/Molecular Complex (sample SD file and result)

Or DNA/RNA Strands (sample PDB file and result)
Single Strand
Double Strand
Auto Detect
Graphic Display None
2D display (GIF)
3D display (requires Chime plug-in, works in Netscape only)
Output Options
Print atom 1' of the sugar.
Print the values of ν04.
Print alpha- or beta-type of nucleoside.
Print sugar pucker (e.g. C2'-endo).
Debug Mode (will print a lot of messages).

Find all sugar moieties, regardless of the base.

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Bug reports, comments or questions?

Last Update: 2011-01-15