Symmetric docking – tetramer of trimers

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    • #891

        I’d like to model a tetramer of trimers. In this situation I’m trying to ensure that all monomers end up on the same X-Y plane. Does anyone have any idea what my symmetry definition file should look like for this? Here’s how I initially tried to do it, but I’m not getting reasonable looking structures:

        symmetry_name sweeden_rules
        subunits 12
        number_of_interfaces 10
        E = 12*VRT0001 + 12*(VRT0001:VRT0002) + 4*(VRT0001:VRT0004) + 4*(VRT0001:VRT0005) + 4*(VRT0001:VRT0006) + 4*(VRT0002:VRT0004) + 4*(VRT0002:VRT0005) + 4*(VRT0002:VRT0006) + 4*(VRT0003:VRT0004) + 4*(VRT0003:VRT0005) + 4*(VRT0003:VRT0006)
        anchor_residue COM
        start -1,0,0 0,1,0 0,0,0
        rot Rz_angle 120.0
        rot Rz_angle 120.0
        # — jump to the 2nd set of trimers
        rot Rz_angle 90.0
        rot Rz_angle 120.0
        rot Rz_angle 120.0
        # — jump to the 3rd set of trimers
        rot Rz_angle 90.0
        rot Rz_angle 120.0
        rot Rz_angle 120.0
        # — jump to the 4th set of trimers
        rot Rz_angle 90.0
        rot Rz_angle 120.0
        rot Rz_angle 120.0
        connect_virtual JUMP1 VRT0001 VRT0002
        connect_virtual JUMP2 VRT0002 VRT0003
        connect_virtual JUMP3 VRT0003 VRT0004
        connect_virtual JUMP4 VRT0004 VRT0005
        connect_virtual JUMP5 VRT0005 VRT0006
        connect_virtual JUMP6 VRT0006 VRT0007
        connect_virtual JUMP7 VRT0007 VRT0008
        connect_virtual JUMP8 VRT0008 VRT0009
        connect_virtual JUMP9 VRT0009 VRT0010
        connect_virtual JUMP10 VRT0010 VRT0011
        connect_virtual JUMP11 VRT0011 VRT0012
        set_dof BASEJUMP x(50) angle_x(0:360) angle_y(0:360) angle_z(0:360)
        set_dof JUMP3 x(50)
        set_dof JUMP6 x(50)
        set_dof JUMP9 x(50)


      • #5560

          While this would generate a tetramer of dimers it would place the subunits on top of each other and translate them in a weird fashion. You have to be able to control the translations within the different trimers (translation relative to their common rotation axis (along z) along their x axis) and translations between trimers in the fourfold. This way one can translate the trimers relative to each other while independently maintaing a certain distance between the subunits within the tetramer. This is done by creating two JUMPGROUPs: One that control the translation/rotation of subunits of relative the trimer rotation axis and one that controls the translation/rotation of the trimers relative to the fourfold axis. One virtual in the trimer has to be master and the other two slaves. Then you have to add jumps to the masters in each trimers. One of these four jumps is made master. Then a jump from one trimer to another (the master) will move all trimers concertedly. However, you cannot have jumps directly beteween trimers because if you translate along those jump directions tetramer would remain the same. Instead the jumps between trimers must be such that there are coordinate systems that are on the origin of the fourfold rotation axis that connect to each trimer and being rotated 90 degrees. This way a translation along this jump from the center of the fourfold to each trimer will move all in a symmetric manner and conserve the fourfold. So on top of the virtuals you have now you should have for extra ones rotated 90 degrees relative to reach other around Z-axis and that jumps to a virtual residue in each trimer (to the master virtual).

          Simple enough ay? Well, a picture would have helped…GLet me know if this does not make any sense and I will make better job at explaining.

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