René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"CIF data incorrect","articleBody":"I use the following code to read CIF files.\n            \n           Structure structure = null;\n          AtomCache cache = new AtomCache();\n          cache.setPath(workdir);\n          cache.setFiletype(StructureFiletype.CIF);\n       \n          StructureIO.setAtomCache(cache);\n      \n          structure = StructureIO.getStructure(pdbFile);\n\nand structure.toMMCIF() to convert into a list of strings. \n\nThe original CIF has HETATM lines as \n\nHETATM 1049 S  S1  . 0KA C 2 .  ? -5.639  -7.082  12.045 1.00 17.18 ? 101 0KA B S1  1 \nHETATM 1051 S  S3  . 0KA C 2 .  ? -6.031  -7.348  15.700 1.00 16.42 ? 101 0KA B S3  1 \nHETATM 1052 S  S4  . 0KA C 2 .  ? -9.120  -7.026  13.781 1.00 13.07 ? 101 0KA B S4  1\n\nBut after reading the CIF, I've\n\nHETATM 1049 S S1 . 0KA C 2 101 ? -5.639 -7.082 12.045 1.00 17.18 101 0KA B S1 1 \nHETATM 1051 S S3 . 0KA C 2 101 ? -6.031 -7.348 15.700 1.00 16.42 101 0KA B S3 1 \nHETATM 1052 S S4 . 0KA C 2 101 ? -9.120 -7.026 13.781 1.00 13.07 101 0KA B S4 1 \n\nThe 9th column in the original CIF is a dot; instead, in the structure object is 101 equals the 16th column (the _atom_site.auth_seq_id).\n\nIs there a way to have the same original HETATM lines in the structure object?","author":{"url":"https://github.com/morellik","@type":"Person","name":"morellik"},"datePublished":"2025-11-06T15:10:02.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":2},"url":"https://github.com/1116/biojava/issues/1116"}