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A brief instruction for running TM-align program:

(For detail, please see Y Zhang, J Skolnick, Nucleic Acids Research, 2005 33: 2302)


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 or to stick the alignment to '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: >rasmol -script TM.sup_all To view superimposed full-atom structures of aligned regions: >rasmol -script TM.sup_atm To view superimposed full-atom structures of all regions: >rasmol -script TM.sup_all_atm To view superimposed full-atom structures of all regions with ligands: >rasmol -script TM.sup_all_atm_lig 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
An example of running TM-align in Linux system (Image of the example can be viewed at here):
    ./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--
An example of running TM-align starting with specific alignment:

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