Only one of the four ambiguous monomers is implemented.

[ClairePA]

It is possible to define a * monomer, but not X, N or _. See the extract below from the HELM specification.

5.1.8. Monomer Ambiguity Unknown monomers can represented by four different characters: • The character “” represents 0..n unknown monomers. • X The character “X” represents one single unknown amino acid in a PEPTIDE polymer. • N The character “N” represents one single unknown base in a RNA polymer. • The character “” represents a deleted or missing single monomer. This is typically used for list elements (see section List Elements)

[scilligence]

fixed in 2017-09-12 update

[ClairePA]

I can't work out how to add X, N or _.

I can add * using the 'monomer attributes' box, but don't know how to add the others.

This method of adding ambiguous monomers is not clear even for *. We need to have a discussion about how the UI works for this example.

[scilligence]

Fixed in 2017-12-1 update

[ClairePA]

I can see *, _ and X as peptide monomers, but nothing under nucleotide or chem.

[scilligence]

Not quite sure what should be used for the ambiguity of nucleotide and chem.

[ClairePA]

Nucleotides should have , _ and N Chem should have .

[scilligence]

Are there some example HELM notations? So we know how to generate the HELM string.

[ClairePA]

RNA1{R()P.R(C)P.(N)P.R(G)P}$$$$V2.0

CHEM1{*}|CHEM2{[sDBL]}|CHEM3{[SMPEG2]}$CHEM2,CHEM3,1:R2-1:R1|CHEM1,CHEM2,1:R1-1:R1$$$V2.0

[scilligence]

2017-12-09 update: * is added to CHEM

[scilligence]

Confirmed in today's meeting:

Base: _, N, Ribose: P: Combo:

[scilligence]

Fixed in 2017-12-13 update

[ClairePA]

Confirmed fixed.