dear modellers, I am wondering what the best approaches are to model complexes using modeller. How would a model best be modelled if: If you have the a pdb file with multiple chains and also multiple unknowns. Is the appropriate way then to make your knowns the different chains and your unknown query one chain separated by '' Or can multiple unknown sequences be used?

you have X different proteins with unknown 3D structure which are homologue with a big protein which has several domains (all in 1 connected chain crystallized). Would the best method be make 1 alligment of your unknown with the crystal and devide the chain by a ''

you have an unknown which is a complex in one amino acid chain and you have a homologue complex which is actually two different chains in the crystal structure. Is the best way in such a case to change the crystal structure to a one chain model? Or simply allign both chains with the one query chain?

kind regards

arnout voet

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