Re: [modeller_usage] R: error using mutate_model.py
To: Anna Marabotti <>
Subject: Re: [modeller_usage] R: error using mutate_model.py
From: Modeller Caretaker <>
Date: Wed, 01 Dec 2010 10:46:06 -0800
Cc:
On 12/01/2010 12:39 AM, Anna Marabotti wrote:
sorry for the missed attachments. However, in the mean time I found the
solution by myself: in the PDB file there was a "TER" after the breaking of
the chain, therefore probably the program interpretates (correctly!) this as
the signal for a new chain (labelled with the same chain ID as the previous
one) instead as of a chain breaking. After removing the TER line, the script
worked properly.
Modeller has no problem with proteins containing multiple chains with
the same ID - the warning is there simply because it will be hard to
refer to the residues or atoms uniquely. For example, if you have two
chains both with ID 'A', then
mdl.residues['10:A']
will give you residue 10 in the *first* chain labeled 'A'. There is no
way to get residue 10 in the *second* chain labeled A using this syntax;
to distinguish them you'd have to refer to the chains numerically
instead, i.e.
mdl.chains[0].residues['10']
and
mdl.chains[1].residues['10']
Since the mutate model script in the wiki uses the first syntax, it
won't be able to find residues in the second chain with the same ID.