[chimerax-users] The ChimeraX-Modeller interface

[Ralph Loring]

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,
Ralph H. Loring
Associate Professor of Pharmacology
Department of Pharmaceutical Sciences
166 TF
Northeastern University
360 Huntington Avenue
Boston, MA 02115 USA
617-373-3216 office
617-373-8886 fax
r.loring at northeastern.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220214/77d0b19d/attachment.html>