I ave a pdb file with only CA coodinate. In order to get a complete strutur I used MDELLER to builld a model. However, the CA atomes were shifted a bit in the model. How can I fix those CA atoms when I build a model? thanks!
Lixia Jin wrote: > I ave a pdb file with only CA coodinate. In order to get a complete > strutur I used MDELLER to builld a model. However, the CA atomes were > shifted a bit in the model. How can I fix those CA atoms when I build a > model?
The CA positions are likely to shift during optimization, but if you really want to fix their positions, you can. See http://salilab.org/modeller/9v1/manual/node22.html for an example of how to optimize only some atoms in the model. In your particular case the selection you want is something like
return selection(self) - selection(self).only_atom_types('CA')
i.e. the selection of "all atoms in the model" minus the selection of "all CA atoms".
Ben Webb, Modeller Caretaker
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Lixia Jin -
Modeller Caretaker