First of all, thanks for all your work on developing software for structural alignments.
I have been using US-align (Version 20241108) guided by sequence alignment as:
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$ ./USalign 1.pdb.gz 2.pdb.gz -infmt1 0 -infmt2 0 -mol RNA -het 1 -seq -outfmt -1 -o <sup-pathfile>Please, could you explain to me line by line how to interpret the results with the following output?
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0 | Name of Structure_1: 1.pdb.gz:? (to be superimposed onto Structure_2)
1 | Name of Structure_2: 2.pdb.gz:?
2 | Length of Structure_1: 16 residues
3 | Length of Structure_2: 15 residues
4 |
5 | User-specified initial alignment: TM/Lali/rmsd = 0.25858, 15, 3.018
6 | Aligned length= 15, RMSD= 3.02, Seq_ID=n_identical/n_aligned= 1.000
7 | TM-score= 0.23648 (normalized by length of Structure_1: L=16, d0=0.50)
8 | TM-score= 0.21836 (normalized by length of Structure_2: L=15, d0=0.40)
9 | (You should use TM-score normalized by length of the reference structure)
10 |
11 | (":" denotes residue pairs of d < 5.0 Angstrom, "." denotes other aligned residues)
12 | aaggagguaaaauucu
13 | .......::::::::
14 | -aggagguaaaauucu
15 |
16 | #Total CPU time is 0.00 seconds
- How should I read the standard output lines for -outfmt -1?
- Why are there 2 values for RMSD, Aligned length and TMscore (line 5 and 6)?
- In line 5 which starts with "User-specified initial alignment: TM/Lali/rmsd..."
- Are those the values that I am looking for?
- Are the RMSD values in lines 5 and 6 the same?
- Why do they have different significant decimals among them and compared to lines 6, 7 and 8?
- Which target sequence length is considered to calculate that 'TM' value (assume TMscore)?
- The 'TM' value in line 5 shouldn't be one of line 7 or 8?
Martín