[modeller_usage] Not refining the CAs of certain residues

[Edelmiro Moman <>]

Hello,

I would like to build protein models in which the CA coordinates of 
certain residues are identical to those of the (single) template.

If I have understood it correctly, the following should do precisely that:

class MyModel(automodel):
    def select_atoms(self):
        # Refine all atoms except the CAs of residues20-40 and 70-80 :
        return selection(self) - selection(self.residue_range('20', 
'40')).only_atom_types('CA')
        return selection(self) - selection(self.residue_range('70', 
'80')).only_atom_types('CA')

Where the residue numbers correspond to those of the model. Is this correct?

Or, if it makes more sense restricting the full backbone of the selected 
residues, would the following work?

class MyModel(automodel):
    def select_atoms(self):
        # Refine all atoms except the backbone atoms of residue 20-40 
and 70-80:
        return selection(self) - selection(self.residue_range('20', 
'40')).only_mainchain()
        return selection(self) - selection(self.residue_range('70', 
'80')).only_mainchain()

Best regards,

Miro

--
Edelmiro Moman, PhD
ProSciens, computer-aided drug design
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L-1841 Luxembourg

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