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A brief instruction for running MM-align program:

(For detail, please see Mukherjee & Zhang, Nucl. Acid. Res. 37:e83, 2009)


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

    Brief instruction for running MM-align program: (For detail: Mukherjee & Zhang, Nucl. Acid. Res. 37:e83, 2009) Please make sure that the two chains of both complexes are seperated by a "TER". 1. Align 'complex1.pdb' to 'complex2.pdb' (By default, TM-score is normalized by the length of 'complex2.pdb') >MMalign complex1.pdb complex2.pdb 2. Run MM-align and output the superposition to 'MM.sup' and 'MM.sup_all': >MMalign complex1.pdb complex2.pdb -o MM.sup To view the superimposed structures of the aligned regions by rasmol: >rasmol -script MM.sup To view the superimposed structures of all regions by rasmol: >rasmol -script MM.sup_all 3. If you want TM-score normalized by an assigned length, e.g. 100 aa: >MDMalign complex1.pdb complex2.pdb -L 100 If you want TM-score normalized by the average length of two structures: >MMalign complex1.pdb complex2.pdb -a If you want TM-score normalized by the shorter length of two structures: >MMalign complex1.pdb complex2.pdb -b If you want TM-score normalized by the longer length of two structures: >MMalign complex1.pdb complex2.pdb -c 4. If you want MM-align to enforce interface alignment defined by a cutoff e.g. 10A : >MMalign complex1.pdb complex2.pdb -I 10 (Distance cutoff is used to determine interface resdiues. Default 8A.) 5. If you want MM-align to allow cross alignment e.g: Domain swap, Gene Fusion : >MMalign complex1.pdb complex2.pdb -DG (First three options,do not change the final structure alignment result)
An example of running MM-align in Linux system:
    ./MMalign complex1.pdb complex2.pdb ************************************************************************** * MM-align * * Aligning protein complex structure by Dynamic Programming * * Comments on the program, please email to: zhng@umich.edu * ************************************************************************** Protein 1:A793697 Size= 186 Protein 2:B793697 Size= 188 (TM-score is normalized by 188) Aligned length= 186, RMSD= 0.83, TM-score=0.96781, ID=0.989 -------- rotation matrix to rotate Chain-1 to Chain-2 ------ i t(i) u(i,1) u(i,2) u(i,3) 1 -7.4207379546 -0.0767574335 0.9970495324 -0.0007254853 2 -8.4709630656 0.0756837691 0.0065520123 0.9971103441 3 -12.9232080011 0.9941731557 0.0764807234 -0.0759633823 (":" denotes the residue pairs of distance < 5.0 Angstrom) t-vwgalghginlnipnfqmtddidevrwergstlvaefkrkpflksgafeilangdlkiknltrddsgtynvtvystngtrildkaldlrileT-VWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: gtvwgalghginlnipnfqmtddidevrwergstlvaefkrkpflksgafeilangdlkiknltrddsgtynvtvystngtrildkaldlrileGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE (Odd no chains of both proteins are in lower case and Even no chains of both proteins are in UPPER case)

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