Dear colleagues,
I want to model a pentamer. I have two templates. One of the templates is arranged anti-clockwise in the order ABCDE. The other template runs clockwise (AEDCB) and has identical chains. Thus if I overlap the two templates, subunit B overlaps with subunit E and so on.
I want to do modelling in 2 steps.
a. I want to get an initial anticlockwise model (ABCDE) from clockwise template (identical chains AEDCB). b. The model obtained from step 1 will be overlapped with the anticlockwise template to build some missing residues.
I tried to get through step a by 1. Changing the alignment file 2. by changing chain identification number in the template 3. by changing the order of subunits arranged in the template
Each time, I end up with the same clockwise model.
Thanks in advance for any kind of suggestion in this regard.
Prema, Graduate student, UOH.
plmallip@mail.uh.edu wrote: > I want to model a pentamer. I have two templates. One of the > templates is arranged anti-clockwise in the order ABCDE. The other > template runs clockwise (AEDCB) and has identical chains. Thus if I > overlap the two templates, subunit B overlaps with subunit E and so on.
Probably the easiest way to do this is to manually edit your clockwise template to put the chains in the same order as in the desired anti-clockwise model. It will be essentially impossible to align the two sequences correctly otherwise. You imply that you tried this already, but I can't tell why it didn't work for you without more information.
(I'm assuming that your alignment between the two templates is C-terminus to C-terminus, N-terminus to N-terminus for each chain. If the sequence in the template is reversed, i.e. C-terminus in template aligns with N-terminus in model, you would have to manually edit the PDB to reverse the sequence.)
Ben Webb, Modeller Caretaker
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plmallip＠mail.uh.edu