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
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm