Lixia Jin Day wrote: > I have a protein conformation with only alpha carbon (CA) atoms. And I > want to build up the full structure without moving the position of the > CA atoms. Can I do it with MODELLER? How to do it?
Did you look at http://salilab.org/modeller/FAQ.html#12 ?
If you don't want to change the protein sequence (i.e. you're not really doing "homology modeling") then you can just feed a Modeller a 1:1 alignment between two copies of the same sequence and use automodel. If you really don't want the CA atoms to move at all, see http://salilab.org/modeller/9v5/manual/node23.html You can use a selection such as s = selection(self) return s - s.only_atom_types('CA')
You could also use complete_pdb() to fill in the non-CA atoms rather than using automodel. But this creates the coordinates from internal coordinates only, so may lead to steric clashes.
Ben Webb, Modeller Caretaker