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error in cyclic design notebook #175

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overlord1647 opened this issue Jun 19, 2024 · 0 comments
Open

error in cyclic design notebook #175

overlord1647 opened this issue Jun 19, 2024 · 0 comments

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@overlord1647
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i am trying to run cyclic peptide using the notebook template provided in afdesign. However i get the following error when i run it:
2 af_model = mk_afdesign_model(protocol="fixbb", data_dir="../params/")
3 model.prep_inputs(pdb_filename="trial_wh_A.pdb", chain="A")
----> 4 add_cyclic_offset(af_model, offset_type=2)

Cell In[43], line 17, in add_cyclic_offset(self, offset_type)
15 c_offset[idx] = (32 * c_offset[idx] )/ abs(c_offset[idx])
16 return c_offset * np.sign(offset)
---> 17 idx = self._inputs["residue_index"]
18 offset = np.array(idx[:,None] - idx[None,:])
20 if self.protocol == "binder":

KeyError: 'residue_index'
the error does not occur when i use getpdb script.

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