how to generate the whole molecule that contains all the symmetric chains

Member Site Forums Rosetta 3 Rosetta 3 – Applications how to generate the whole molecule that contains all the symmetric chains

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    • #2807
      Anonymous

        Dear all,

        I have a pdb file which contains three chains (A, B, and C) for a protein molecule. According to my knowledge, the protein should be 3-fold symetric and a trimer of the three chains. Is there a way to generate the pdb file which contains all the 9 chains for the whole molecules?  I can only find some infomation from the original pdb file about the symmetry like these:

        REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            

        REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63                             

        REMARK 290                                                                      

        REMARK 290      SYMOP   SYMMETRY                                                

        REMARK 290     NNNMMM   OPERATOR                                                

        REMARK 290       1555   X,Y,Z                                                   

        REMARK 290       2555   -Y,X-Y,Z                                                

        REMARK 290       3555   -X+Y,-X,Z                                               

        REMARK 290       4555   -X,-Y,Z+1/2                                             

        REMARK 290       5555   Y,-X+Y,Z+1/2                                            

        REMARK 290       6555   X-Y,X,Z+1/2                                             

        REMARK 290                                                                      

        REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     

        REMARK 290           MMM -> TRANSLATION VECTOR                                  

        REMARK 290                                                                      

        REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            

        REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             

        REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                

        REMARK 290 RELATED MOLECULES.                                                   

        REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            

        REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            

        REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            

        REMARK 290   SMTRY1   2 -0.500000 -0.866025  0.000000        0.00000            

        REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            

        REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000            

        REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            

        REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            

        REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            

        REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000        0.00000            

        REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000            

        REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       46.88850            

        REMARK 290   SMTRY1   5  0.500000  0.866025  0.000000        0.00000            

        REMARK 290   SMTRY2   5 -0.866025  0.500000  0.000000        0.00000            

        REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       46.88850            

        REMARK 290   SMTRY1   6  0.500000 -0.866025  0.000000        0.00000            

        REMARK 290   SMTRY2   6  0.866025  0.500000  0.000000        0.00000            

        REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       46.88850  

         

        Can rosetta do the job as I need?

        Best regards.

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