SAXS

[Guenter]

Dear Bunch developers and users,
This question has to do with a specific domain arrangement of a homodimer that I would like to explore with Bunch. An N-terminal domain and a C-terminal domain form this specific dimer. The domain in the middle, however, is not involved in protein-protein contacts and there are mobile linkers between N- and middle domains as well as middle and C-terminal domains. This means that a two-fold symmetry can only be defined in either only the N-terminal domain or the C-terminal domain (i.e. both have different symmetry axes). Running Bunch with two-fold symmetry constraint is therefore not providing the correct picture.
Thus in my present Bunch runs I am keeping the N-terminal domains fixed (to maintain their domain interaction characteristics) and let all the other domains move “freely”. In order to preserve interactions in the dimer formed by the C-terminal domains I have defined a contacts condition file as constraint. This ought to do the job, I thought... But looking at the produced result and comparing it with the initial structure it became clear that not only the (position of the) N-terminal domains dimer remains unchanged (as defined) but also one of the C-terminal domains does not change its spatial position at all (i.e. limiting the exploration of spatial positions of the C-terminal dimer severely) thus behaving like a fixed subunit in coordinate space (even though having defined it to be mobile). Is there a difficulty with Bunch in running this particular arrangement? Could there be a problem with regards to the definition of the centre of mass or the contacts condition file, which causes one of the C-terminal domains not deviating from its initial position? I would be very grateful for any advice you can give me. Thank you very much in advance.

[SaxsMax]

It is not very clear if you finally used the symmetry constraint or not.
By design, Bunch is only able to handle the cases with one chain per
asymmetric part, i.e. the dimer must be run with P2 symmetry which imposes that the two-fold axes of N- and C- termini coincide.
We plan to distribute a new program in the next release of Atsas
which would be able to handle complicated cases like yours.
One more thing about Bunch: the length of the linkers must be
at least four DRs otherwise some domains may stuck though they
were not fixed.