I type the HELM
PEPTIDE1{A.A.A.A.A.C.D.D.D.D.D.E.E.E.E}|PEPTIDE2{G.G.G.C.S.S.S.S.S.P.P.K.K.K.K}|CHEM1{[PEG2]}|CHEM2{[SMCC]}$PEPTIDE1,CHEM1,C:R3-1:R1|PEPTIDE2,CHEM2,C:R3-1:R1$G1(PEPTIDE1+CHEM1:2.5)|G2(PEPTIDE2+CHEM2:1.5)$$V2.0 onto the HELM canvas and click apply.
I type the HELM
PEPTIDE1{A.A.A.A.A.C.D.D.D.D.D.E.E.E.E}|PEPTIDE2{G.G.G.C.S.S.S.S.S.P.P.K.K.K.K}|CHEM1{[PEG2]}|CHEM2{[SMCC]}$PEPTIDE1,CHEM1,C:R3-1:R1|PEPTIDE2,CHEM2,C:R3-1:R1$G1(PEPTIDE1+CHEM1:2.5)|G2(PEPTIDE2+CHEM2:1.5)$$V2.0
onto the HELM canvas and click apply.The structure is displayed,
PEPTIDE1{A.A.A.A.A.C.D.D.D.D.D.E.E.E.E}|PEPTIDE2{G.G.G.C.S.S.S.S.S.P.P.K.K.K.K}|CHEM1{[PEG2]}|CHEM2{[SMCC]}$PEPTIDE1,CHEM1,C:R3-1:R1|PEPTIDE2,CHEM2,C:R3-1:R1$G1(PEPTIDE1+CHEM1:2.5)|G2(PEPTIDE2+CHEM2:1.5)$$V2.0
The ratios have been swapped over. See below to see the problematic section highlighted.