Hi,
Jenny.Carmichael@csiro.au wrote: > > Dear Modellers, > I am a new user of modeller having just completed my PHD in X-ray crystallography. I have two questions about modeller. > 1) Do the template positions of domains in space, for multidomain proteins, have to always be pre-arranged/aligned by me to the approximate postions of the putative model before running modeller ?
yes.
> 2) In a way this is similar to the first question. How can I model the possible linker flexibility in a diabody ? > I would need to fix the atom positions in each Fv with respect to each other but not thier actual coordinates, whilst allowing a variety of linker models to be built.
if you use loop modeling it assumes that the stem residues and environment (i.e. the two domains) are fixed, and only the loop is optimized. The domains do not move with respect to each other. Modeller uses the interdomain nonbonded distance restraints as they are derived from the input conformation, i.e. the domain orientation does not change too much during modeling.
if you are looking for domain movement modeling: Modeller is not a trivial tool for that, but it is possible. A quick and dirty solution is to break up your template into two, non overlapping parts, at the linker site, and use them as separate templates. By this way modeller will not derive interdomain restraints, because there is no overlap. However the outcome of modeling, especially with longer linker regions, can be quite uncertain. This is a kind of 'ab initio' modeling of domain placement.
Andras