PDB声明链序列导出

操作示例

示例输入

SEQRES   1 A   21  GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU
SEQRES   2 A   21  TYR GLN LEU GLU ASN TYR CYS ASN
SEQRES   1 B    3  MSE UNK ALA
MODRES 1ABC MSE B    1  MET  SELENOMETHIONINE

{"secondary":"","params":{"chainMode":"all","chainId":"A","spreadsheetSafe":true}}

示例输出

{"format":"legacy-PDB3.3-protein-SEQRES","summary":{"inputLines":4,"inputChains":2,"inputResidues":24,"selectedChains":2,"selectedResidues":24,"unknownResidues":1,"status":"declared-sequences"},"chainEncoding":"FASTA identifier chain-uXXXX encodes the original printable ASCII code point in uppercase hexadecimal; blank is chain-u0020.","chains":[{"chain":"A","chainCode":65,"declaredCount":21,"lastSerial":2,"residues":[{"position":1,"name":"GLY","parent":"GLY","letter":"G","status":"standard","line":1,"column":20},{"position":2,"name":"ILE","parent":"ILE","letter":"I","status":"standard","line":1,"column":24},{"position":3,"name":"VAL","parent":"VAL","letter":"V","status":"standard","line":1,"column":28},{"position":4,"name":"GLU","parent":"GLU","letter":"E","status":"standard","line":1,"column":32},{"position":5,"name":"GLN","parent":"GLN","letter":"Q","status":"standard","line":1,"column":36},{"position":6,"name":"CYS","parent":"CYS","letter":"C","status":"standard","line":1,"column":40},{"position":7,"name":"CYS","parent":"CYS","letter":"C","status":"standard","line":1,"column":44},{"position":8,"name":"THR","parent":"THR","letter":"T","status":"standard","line":1,"column":48},{"position":9,"name":"SER","parent":"SER","letter":"S","status":"standard","line":1,"column":52},{"position":10,"name":"ILE","parent":"ILE","letter":"I","status":"standard","line":1,"column":56},{"position":11,"name":"CYS","parent":"CYS","letter":"C","status":"standard","line":1,"column":60},{"position":12,"name":"SER","parent":"SER","letter":"S","status":"standard","line":1,"column":64},{"position":13,"name":"LEU","parent":"LEU","letter":"L","status":"standard","line":1,"column":68},{"position":14,"name":"TYR","parent":"TYR","letter":"Y","status":"standard","line":2,"column":20},{"position":15,"name":"GLN","parent":"GLN","letter":"Q","status":"standard","line":2,"column":24},{"position":16,"name":"LEU","parent":"LEU","letter":"L","status":"standard","line":2,"column":28},{"position":17,"name":"GLU","parent":"GLU","letter":"E","status":"standard","line":2,"column":32},{"position":18,"name":"ASN","parent":"ASN","letter":"N","status":"standard","line":2,"column":36},{"position":19,"name":"TYR","parent":"TYR","letter":"Y","status":"standard","line":2,"column":40},{"position":20,"name":"CYS","parent":"CYS","letter":"C","status":"standard","line":2,"column":44},{"position":21,"name":"ASN","parent":"ASN","letter":"N","status":"standard","line":2,"column":48}],"sequence":"GIVEQCCTSICSLYQLENYCN"},{"chain":"B","chainCode":66,"declaredCount":3,"lastSerial":1,"residues":[{"position":1,"name":"MSE","parent":"MET","letter":"M","status":"MODRES-mapped","line":3,"column":20},{"position":2,"name":"UNK","parent":"UNK","letter":"X","status":"unknown-residue","line":3,"column":24},{"position":3,"name":"ALA","parent":"ALA","letter":"A","status":"standard","line":3,"column":28}],"sequence":"MXA"}],"modres":[{"line":4,"chain":"B","name":"MSE","parent":"MET"}],"scope":"Declared SEQRES only, no ATOM fallback/observed-residue/biological validation. 20 standard amino acids plus ASX/GLX/UNK; unique MODRES chain+name mapping. Unknown three-character names become X with source positions. Nucleotides/mmCIF unsupported."}

出现问题时

检查ASCII legacy PDB固定列、三字符蛋白残基槽、连续serial、恒定且匹配的numRes和无歧义MODRES parent；选择现有链。mmCIF/核酸等不支持数据应由原工具重新导出。

常见问题