解析TMalign结构比对结果

TM-align 将两个蛋白质结构通过旋转和位移对齐后：

TMalign 6owd_A.pdb  6owd_B.pdb -m 6owd_AB_mtx.txt 1>output.txt

屏幕输出内容，可以重定向为文件，文件内容为：

 *********************************************************************
 * TM-align (Version 20220412): protein structure alignment          *
 * References: Y Zhang, J Skolnick. Nucl Acids Res 33, 2302-9 (2005) *
 * Please email comments and suggestions to zhanglab@zhanggroup.org   *
 *********************************************************************

Name of Chain_1: 6owd_A.pdb (to be superimposed onto Chain_2)
Name of Chain_2: 6owd_B.pdb
Length of Chain_1: 28 residues
Length of Chain_2: 28 residues

Aligned length= 27, RMSD=   0.80, Seq_ID=n_identical/n_aligned= 0.000
TM-score= 0.85914 (if normalized by length of Chain_1, i.e., LN=28, d0=1.12)
TM-score= 0.85914 (if normalized by length of Chain_2, i.e., LN=28, d0=1.12)
(You should use TM-score normalized by length of the reference structure)

(":" denotes residue pairs of d <  5.0 Angstrom, "." denotes other aligned residues)
-QIARLQRQIRALQRQNARLQRQIRALQW
 ::::::::::::::::::::::::::: 
QIARLQRQIRALQRQNARLQRQIRALQW-

Total CPU time is  0.00 seconds

输出结果解释

• Aligned length：两个结构的对齐长度为 27 个残基，这意味着虽然每条链都有 28 个残基，但比对过程中只有 27 个残基是成功对齐的。