The CTERM_AMIDATION has some issues that make working with it challenging. For one, it removes too many properties, making it difficult to select the terminal residue. I have also encountered errors when trying to use it in combination with NCAAs, though I think @roccomoretti may have fixed that aready.
Here is a C-terminal alanine with and without capping:
Vanilla:
Base: ALA
Properties: POLYMER PROTEIN CANONICAL_AA UPPER_TERMINUS ALIPHATIC METALBINDING ALPHA_AA L_AA
Variant types: UPPER_TERMINUS_VARIANT
Capped:
Base: ALA
Properties: POLYMER PROTEIN ALIPHATIC METALBINDING ALPHA_AA L_AA
Variant types: CTERM_AMIDATION
In contrast, this problem does not exist with ACETYLATED_NTERMINUS_VARIANT, which retains the LOWER_TERMINUS property and gains an ACETYLATED_NTERMINUS property.
Vanilla:
Base: ALA
Properties: POLYMER PROTEIN CANONICAL_AA LOWER_TERMINUS ALIPHATIC METALBINDING ALPHA_AA L_AA
Variant types: LOWER_TERMINUS_VARIANT
Capped:
Base: ALA
Properties: POLYMER PROTEIN CANONICAL_AA LOWER_TERMINUS ALIPHATIC METALBINDING ACETYLATED_NTERMINUS ALPHA_AA L_AA
Variant types: ACETYLATED_NTERMINUS_VARIANT
Andy Watkins mentioned that METHYLATED_CTERMINUS_VARIANT works well, so that may be a good template for comparison.
The CTERM_AMIDATION has some issues that make working with it challenging. For one, it removes too many properties, making it difficult to select the terminal residue. I have also encountered errors when trying to use it in combination with NCAAs, though I think @roccomoretti may have fixed that aready.
Here is a C-terminal alanine with and without capping:
Vanilla:
Capped:
In contrast, this problem does not exist with ACETYLATED_NTERMINUS_VARIANT, which retains the LOWER_TERMINUS property and gains an ACETYLATED_NTERMINUS property.
Vanilla:
Capped:
Andy Watkins mentioned that METHYLATED_CTERMINUS_VARIANT works well, so that may be a good template for comparison.