Re: [modeller_usage] how to make models with sulfide connection information ?
To: Mahesh Velusamy <>,
Subject: Re: [modeller_usage] how to make models with sulfide connection information ?
From: Modeller Caretaker <>
Date: Mon, 27 Jul 2015 15:45:53 -0700
On 07/10/2015 09:31 AM, Mahesh Velusamy wrote:
I have a template structure called 3O26 which has two sulfide connections:
SSBOND 1 CYS A 263 CYS A 305 1555 1555
2.04
CONECT 1934 2256
CONECT 2256 1934
Modeller doesn't read SSBOND or CONECT records to determine disulfide
bridges - it just looks at the geometry (distance between the two SG atoms).
If the target sequence has a pair of cysteine residues aligned to a pair
of cysteine residues that form a disulfide bridge in any of the homologous
structures, then a disulfide bond will be expected in the model structure
and the necessary constraints will be defined automatically. Anticipated
disulfide bonds are reported in the log file.
Note that for this to work both CYS residues in the template must be
aligned with CYS residues in the target.
PATCH RESIDUE_TYPE = `DISU', RESIDUE_IDS = n1 n2 # Here I have a doubt
that SHOULD I mention the n1 n2 from the template or MODELS ? (for ex in
my case 3O26: n1=263 and n2=305).
This is ancient pre-Python Modeller syntax, but residue IDs always refer
to the models. It would make no sense to use template numbering here.
Here When I mentioned the residues from template like above I got a
following ERROR
KeyError: 'No such residue: 44:D'
Like the error says, there is no residue with index 44 in chain D. Look
at the model you built already without disulfides and verify the correct
residue numbering.