Secondary structure database

Under the hood, pmlbeta maintains a database of secondary structures, which is essentially a bunch of backbone dihedral angle triplets with labels. This is stored in the form of a Python dict, mapping string labels to tuples of floating point numbers.

By default the following are defined:

DEFAULT_HELIXTYPES = {
    'Z6M': (126.7, 62.6, 152.7),
    'Z6P': (-126.7, -62.6, -152.7),
    'Z8M': (47.5, 53.5, -104.3),
    'Z8P': (-47.5, -53.5, 104.3),
    'H8M': (76.8, -120.6, 52.7),
    'H8P': (-76.8, 120.6, -52.7),
    'H10M': (-77.5, -51.8, -75.1),
    'H10P': (77.5, 51.8, 75.1),
    'H12M': (92.3, -90.0, 104.6),
    'H12P': (-92.3, 90.0, -104.6),
    'H14M': (-140.3, 66.5, -136.8),
    'H14P': (140.3, -66.5, 136.8),
    'SM': (70.5, 176.2, 168.9),
    'SP': (-70.5, -176.2, -168.9),
    'Straight': (180, 180, 180),
    'Straight alpha': (180, None, 180),
    'Alpha-helix': (-57, None, -47),
    '3_10-helix': (-49, None, -26),
    'P-beta-sheet': (-119, None, 113),
    'AP-beta-sheet': (-139, None, 135),
}

Corresponding to the following:

Abbreviation phi theta psi Comments
Z6M 126.7° 62.6° 152.7° from Beke et. al.(2006)
Z6P -126.7° -62.6° -152.7°
Z8M 47.5° 53.5° -104.3°
Z8P -47.5° -53.5° 104.3°
H8M 76.8° -120.6° 52.7°
H8P -76.8° 120.6° -52.7°
H10M -77.5° -51.8° -75.1°
H10P 77.5° 51.8° 75.1°
H12M 92.3° -90.0° 104.6°
H12P -92.3° 90.0° -104.6°
H14M -140.3° 66.5° -136.8°
H14P 140.3° -66.5° 136.8°
SM 70.5° 176.2° 168.9°
SP -70.5° -176.2° -168.9°
Straight 180° 180° 180°  
Straight alpha 180° 180°
Alpha-helix -57° -47° from PyMOL
P-beta-sheet -119° 113°
AP-beta-sheet -139° 135°
3_10-helix -49° -26°  

Editing this list is possible by the corresponding GUI utility, or by the ssdb_* commands.

Changes to the secondary structure database are remembered in the next PyMOL session.

Python API documentation