betafab2

pmlbeta.betafab2.betafab2(objname, *args)[source]

Construct an alpha/beta peptide

Amino acids can be given in the following way:

  1. beta-2 amino-acid:
    ({S|R})B2h<sc> e.g. (S)B2hV, (R)B2hA
  2. beta-3 amino-acid:
    ({S|R})B3h<sc> e.g. (S)B3hL, (R)B3hR
  3. beta-2,3 amino-acid:
    (2{S|R}3{S,R})B23h(2<sc1>3<sc2>) e.g. (2S3R)B23h(2A3L)
  4. bare beta-backbone:
    BA or (2S3R)B23h(2G3G) (with any combination of R and S
    in the first pair of parentheses)
  5. alpha-amino acid:
    ({S|R|L|D})A<sc> e.g. (S)AL, (R)AV, (L)AA, (D)AC
  6. capping groups:
    ACE: acetyl on the N-terminus (must be first) BUT: butyl on the N-terminus (must be first) NME: N-methylamide on the C-terminus (must be last)
  7. cyclic beta-residues:
    (2{S|R}3{S|R})ACHC (2-aminocyclohexanecarboxylic acid) e.g. (2S3R)ACHC (2{S|R}3{S|R})ACPC (2-aminocyclopentanecarboxylic acid) e.g. (2S3R)ACPC

where <sc> is the single-letter abbreviation of a natural peptide sidechain. The following are supported:

A, C, D, E, F, G, I, K, L, M, N, O, Q, R, S, T, V, W, Y.
In addition, the following variants are also understood:
CM :
deprotonated cysteine
DH :
aspartic acid
EH :
glutamic acid
HD :
histidine protonated on the delta-nitrogen
HE :
histidine protonated on the epsilon-nitrogen
HH :
histidine protonated on both nitrogens
KN :
neutral lysine
ON :
neutral ornithine

The desired secondary structure can be given as well after each amino-acid in two possible ways:

  1. three (or two) floating point numbers in square brackets, e.g. (S)AQ[-57 -47] or (S)B3hV[-140.3 66.5 -136.8]
  2. referencing an entry of the secondary structure database in curly braces, e.g. (S)AQ{Alpha-helix} or (S)B3hV{H14M}
Parameters:
  • objname (str) – the name PyMOL will know about the resulting peptide
  • args (str) – amino-acid abbreviations
Returns:

the constructed peptide
Return type:

BetaPeptide