Welcome
This area will be developed as a way of capturing best practices when using the HELM notation.
Please do let us know if you have an item you would like to add, or a question on HELM. You can use the issue list or email us at info@openHELM.org or just add a comment to the end of this page!
Handling monomers in lists
HELM allows users to specify lists of alternative monomers or mixtures in any order. So PEPTIDE1{(A+dA)}$$$$V2.0 and PEPTIDE1{(dA+A)}$$$$V2.0 are exactly the same. However this can get confusing when there are long lists of monomers and also make comparisons between HELM strings more difficult.
Recommendation: Put monomers in alphabetical order when using them in lists.
HELM allows users to add the same monomer more than once in a list. So PEPTIDE1{(A+A+L+L+A+V)}$$$$V2.0 is allowed.
However, there is no point to doing this as the notation assumes that the ratio of the components are unknown if the proportions are not specified: PEPTIDE1{(A+A+L+L+A+V)}$$$$V2.0 is exactly the same as PEPTIDE1{(A+L+V)}$$$$V2.0. and the latter example is much clearer to read.
If you want to specify proportions, you should use PEPTIDE1{(A:3+L:3+V:1)}$$$$V2.0
Recommendation: Don't use the same monomer more than once in a list.