Error: Cannot parse file

[agarrubio]

Hello!

The current version of TMalign (20210520) cannot parse my pdb: "Warning! Cannot parse file: ecoli/tmp/AF-P31468-Q_48_154.pdb. Chain number 0." However, the pdb works fine in the web server:

https://seq2fun.dcmb.med.umich.edu//TM-align/

Also, it is valid in chimerax, and is aproved by pdb_validate and pdb_tidy from pdb_tools.

What could be the issue?

The pdb is at: https://drive.google.com/file/d/1SpDfNZEqzGVpuP0mgS8dRwasMQtr7q-B/view?usp=sharing

Many thanks

[kad-ecoli]

In your example, all atom names are left justified, causing C-alpha atoms " CA " to be incorrectly named as calcium atoms "CA " at columns 13-16 of the PDB file. If you have to parse the file, you can specify the atom name as "CA ":

TMalign AF-P31468-Q_48_154.pdb AF-P31468-Q_48_154.pdb -atom "CA  "

 **********************************************************************
 * TM-align (Version 20210520): protein and RNA structure alignment   *
 * References: Y Zhang, J Skolnick. Nucl Acids Res 33, 2302-9 (2005)  *
 *             S Gong, C Zhang, Y Zhang. Bioinformatics, bz282 (2019) *
 * Please email comments and suggestions to yangzhanglab@umich.edu    *
 **********************************************************************

Name of Structure_1: AF-P31468-Q_48_154.pdb (to be superimposed onto Structure_2)
Name of Structure_2: AF-P31468-Q_48_154.pdb
Length of Structure_1: 107 residues
Length of Structure_2: 107 residues

Aligned length= 107, RMSD=   0.00, Seq_ID=n_identical/n_aligned= 1.000
TM-score= 1.00000 (normalized by length of Structure_1: L=107, d0=3.80)
TM-score= 1.00000 (normalized by length of Structure_2: L=107, d0=3.80)
(You should use TM-score normalized by length of the reference structure)

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

Please also note that TM-align is a legacy program. You should use US-align instead.