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PistoiaHELM / HELMWebEditor

Web browser based editor for drawing HELM macromolecules.
MIT License
18 stars 10 forks source link

Not sure how to add monomer alternatives or mixtures #147

Closed ClairePA closed 6 years ago

ClairePA commented 6 years ago

The HELM design document includes the following:

Missing monomer In some cases, a position can be occupied by a monomer or not. Example: A trailing Lysine might be present at the C-terminus of an antibody or not. An underscore is used to denote a potential blank position.

PEPTIDE1{A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.(_,K)}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$

Single Monomer – no probability Any single monomer of a list may be found at given position. The list elements are separated by a comma and grouped using parentheses. No probability for the occurrence of a distinct monomer is given.

PEPTIDE1{A.A.A.A.(A,G,W,[Aha]).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$

Single Monomer with probability Any single monomer of a list may be found at given position, probability of occurrence of given monomer within that list is known, but product contains exactly one monomer.

PEPTIDE1{A.A.A.A.(A:1.1,G:69.5,W:25.5,[Aha]:3.9).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$

The chromatogram of a sequence doesn’t allow to define exactly which monomer is available a certain position. But it allows giving information about the probability for the potential monomers. Monomer mixture A mixture of monomers of a list may be found at given position.

PEPTIDE1{A.A.A.A.(A+G+W+[Aha]).A.(A+G).A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$

Monomer mixture with ratios A mixture of monomers of a list may be found at given position, ratio of monomers within that list is known.

PEPTIDE1{A.A.A.A.(A:1.1+G:69.5+W:25.5+[Aha]:3.9).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$

Mixture of 4 proteins with differing monomers at positions 5 and 10. 10% PEPTIDE1{A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D. 40% PEPTIDE1{A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D. 10% PEPTIDE1{A.A.A.A.A.A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D. 40% PEPTIDE1{A.A.A.A.G.A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.

Resulting HELM string with ambiguity notation: PEPTIDE1{A.A.A.A.(A+G).A.A.A.A.(A+G).A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.

Unknown monomer Unknown monomers (0..n monomers) may be found at given position.

PEPTIDE1{A.A.A.A.*.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$

Unknown monomers (1..n monomers) may be found at given position. PEPTIDE1{A.A.A.A.(X,*).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$

Unknown monomers (1) may be found at given position in PEPTIDE. PEPTIDE1{A.A.A.A.X.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$

Unknown monomers (1) may be found at given position in RNA. RNA1{R(A)P.R(G)P.R(N)P.R(A)P}$$$

I am not sure how to enter examples like these into the editor.

ClairePA commented 6 years ago

Confirmed present in the user guide. Close.