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.
Ben Webb, Modeller Caretaker