Hi,

The intracellular domain (ICD) of Alpha7 nicotinic receptors, like almost all eukaryotic Cys-loop receptors, is not resolved using X-ray crystallography or  cryo-EM.  Last week the PDB for an ensemble of NMR ICD structures for the receptor was released (PDB 7RPM).  I've been unsuccessfully trying to use ChimeraX and Modeller to make a model of a subunit that includes the ICD.  The 7RPM models include all 4 transmembrane domains and the ICD (but lacks the extracellular domain), so there is considerable overlap with the 7KOO PDB fo
a7.  I started by deleting  all but one of the identical subunits in the 7KOO pdb and loaded one of the 7RPM models and tried to use Modeller to make a construct that includes both the extracellular domain and the ICD.  Unfortunately, even though both 7KOO and the single 7RPM are in the sequence alignments window, the ChimeraX-Modeller combination ignores the structure that is not chosen as the target (e.g. if 7RPM is the target, there is no extracellular domain, but if 7KOO is the target, there is either no ICD or the ICD that is shown bears no relevance to the structure in 7RPM).  I can align the two structures well with a low RMSD using Matchmaker because of the TMDs overlapping.  I just want to fill in the missing parts.  Is there a special trick to get Modeller to fill in the missing parts using ChimeraX as the interface? I'm not that experienced using Modeller.

Thanks,