Brief instruction (you can obtain the same information by running TM-align program without argument)

 1. Align 'chain_1.pdb' and 'chain_2.pdb':
    >TMalign chain_1.pdb chain_2.pdb

 2. Ask TM-align to start with an alignment specified in fasta file 'align.txt':
    >TMalign chain_1.pdb chain_2.pdb -i align.txt

 3. Output the superposition to 'TM.sup', 'TM.sup_all' and 'TM.sup_atm':
    >TMalign chain_1.pdb chain_2.pdb -o TM.sup
       To view superimposed C-alpha traces of aligned regions by rasmol:
         >rasmol -script TM.sup
       To view superimposed C-alpha traces of all regions by rasmol:
         >rasmol -script TM.sup_all
       To view superimposed full-atom structures of all regions by rasmol:
         >rasmol -script TM.sup_atm

 4. There are two TM-scores reported. You should use the one normalized by
    the length of the protein you are interested in.
    If you want TM-score normalized by the average length of two proteins:
       >TMalign chain_1.pdb chain_2.pdb -a
    or TM-score normalized by an assigned length (>L_min), e.g. 100 AA:
       >TMalign chain_1.pdb chain_2.pdb -L 100
    If you want TM-score scaled by an assigned d0, e.g. 5 A:
       >TMalign chain_1.pdb chain_2.pdb -d 5

 5. Output TM-align rotation matrix:
    >TMalign chain_1.pdb chain_2.pdb -m matrix.txt

./TMalign model1.pdb model2.pdb

 **************************************************************************
 * TM-align (Version 20120419): A protein structural alignment algorithm  *
 * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005)    *
 * Please email your comments and suggestions to: zhng@umich.edu          *
 **************************************************************************

Name of Chain_1: model1.pdb                                     
Name of Chain_2: model2.pdb                                     
Length of Chain_1:   97 residues
Length of Chain_2:   89 residues

Aligned length=   85, RMSD=   2.92, Seq_ID=n_identical/n_aligned= 0.071
TM-score= 0.61968 (if normalized by length of Chain_1)
TM-score= 0.65866 (if normalized by length of Chain_2)
(You should use TM-score normalized by length of the reference protein)

(":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues)
TNQKTKELSNLIETFAEQSRVLEKECTKIGSK----RDSKELRYKIETELIPNCTSVRDKIESNILIHQNGKLSADFKNLKTKYQSLQQSYNQRKSLFPLK
     .  :::::::::::::::::::::.::    .:::::::::: :::::::::::::::::...::: ::: ::::::::::::::::::::::.  
-----E--DPFQQVVKDTKEQLNRINNYITRHNTADDQEEEIQDILK-DVEETIVDLDRSIIVMKRDENED-VSG-REAQVKNIKQQLDALKLRFDRRI--

(In case that TM-align does not generate the optimal alignment, assigning an appropriate alignment can improve the final alignment results of TM-align, as shown in the example below)

./TMalign model1.pdb model2.pdb -i align.txt

 **************************************************************************
 * TM-align (Version 20120419): A protein structural alignment algorithm  *
 * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005)    *
 * Please email your comments and suggestions to: zhng@umich.edu          *
 **************************************************************************

Name of Chain_1: model1.pdb                                     
Name of Chain_2: model2.pdb                                     
Length of Chain_1:   97 residues
Length of Chain_2:   89 residues
User-specified initial alignment: TM/Lali/rmsd= 0.66740,   81,  2.116

Aligned length=   82, RMSD=   2.01, Seq_ID=n_identical/n_aligned= 0.136
TM-score= 0.69535 (if normalized by length of Chain_1)
TM-score= 0.70780 (if normalized by length of Chain_2)
(You should use TM-score normalized by length of the reference protein)

(":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues)
TNQKTKELSNLIETFAEQSRVLEKECTKIGSKRDSKELR-YKIETELIPNCTSVRDKIESN-I-LIH-----QNGKLSADFKNLKTKYQSLQQSYNQRKSLFPLK
    :::::::::::::::::::::::::::   .: :: ::::: ::::::::::::::: : ::      :::::::::::::::::::::::::::      
----EDPFQQVVKDTKEQLNRINNYITRHNT---AD-DQEEEIQD-ILKDVEETIVDLDRSIIVMK-RDENEDVSGREAQVKNIKQQLDALKLRFDRRI------