Addaa adds an amino acid of type res_type with sequence number res_number after preceding_res, which must be the last residue of a chain. The preceding_res specification may contain just a part of that residue (such as one atom or bond) but not more than one residue. Res_type is a three-letter residue name for one of the 20 standard amino acids (case is unimportant). Res_number can include an insertion code.
The conformation can be specified with a keyword:
| keyword | description | phi (deg) | psi (deg) |
|---|---|---|---|
| ext | extended (default) | 180 | 180 |
| alpha | alpha helix | -57 | -47 |
| abeta | parallel beta sheet | -139 | 135 |
| pbeta | antiparallel beta sheet | -119 | 113 |
or with a comma-separated pair of values:
phi,psi(the desired phi and psi angles in degrees).
An added residue may not have an optimal geometry and may clash with other parts of the structure. Residues added with the alpha keyword are given the attribute isHelix=true; those added with the abeta or pbeta keyword are given the attribute isStrand=true (isSheet=true). However, the backbone dihedral angles are merely those appropriate for the designated conformational state and do not ensure that the added residue will fall within that type of secondary structure (which depends on the conformations of multiple residues). One way to evaluate secondary structure after building is complete is to run ksdssp.
The temperature factor for the new residue is set to the highest currently found in the model.
Example:
addaa tyr,30 :29.a- add tyrosine in an extended conformation as residue 30, after residue 29 in chain A (the new residue will also be in chain A)