From f5f6b03b61f77fce7108ab04d363ec60ffc64db4 Mon Sep 17 00:00:00 2001 From: Ezra Peisach Date: Wed, 13 Nov 2024 08:45:32 -0500 Subject: [PATCH] set defaults as acetylation/amidation for ACE/NH2 --- wwpdb/apps/seqmodule/align/AlignmentTools.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/wwpdb/apps/seqmodule/align/AlignmentTools.py b/wwpdb/apps/seqmodule/align/AlignmentTools.py index 7e90a64..a26718c 100644 --- a/wwpdb/apps/seqmodule/align/AlignmentTools.py +++ b/wwpdb/apps/seqmodule/align/AlignmentTools.py @@ -1215,6 +1215,8 @@ def __annotateConflictingComments(self, authIdx, refIdx, beg_pos, end_pos, write if self._seqAlignList[i][refIdx][1] == self._gapSymbol: if (i == 0) and (self._seqAlignList[i][authIdx][1] in ("MET", "MSE")): comment = "initiating methionine" + elif (i == 0) and (self._seqAlignList[i][authIdx][1] == "ACE"): + comment = "acetylation" elif i < first_pair_position: if first_fragment: comment = "expression tag" @@ -1223,7 +1225,11 @@ def __annotateConflictingComments(self, authIdx, refIdx, beg_pos, end_pos, write # elif i > last_pair_position: if last_fragment: - comment = "expression tag" + if (i == end_pos) and (self._seqAlignList[i][authIdx][1] == "NH2"): + comment = "amidation" + else: + comment = "expression tag" + # else: comment = "linker" #