Superimpose two proteins
ı tried superimposed two protein with different size
But get error when ı run
line 27, in <module> superimposer.set_atoms(query_atoms, target_atoms)
line 36, in set_atoms
raise PDBException("Fixed and moving atom lists differ in size")
Bio.PDB.PDBExceptions.PDBException: Fixed and moving atom lists differ in size
Here ı understand my query is 366 and target atoms is 284 length
how ı can solve this problem ? thank you
Do they have the same fold ? Whats' the blast percentage identity between the two ?
I only remember calculating RMS from two superimposed proteins in UCSF Chimera I think (that was ages ago).
But shouldn't you be doing a very important pairwise alignment first ? Think I used MODELLER for this.
I'd advise just using the MatchMaker tool in
UCSF Chimera. It's a very matured implementation at this stage, and will handle proteins of different sizes etc.
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