Reply To: Symmetric docking – tetramer of trimers

[Anonymous]

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.