[modeller_usage] Re: CONECT records writing mutated PDB

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 9/13/23 8:51 AM, Pedro Guillem via modeller_usage wrote:
> I use Modeller to induce point mutations on a PDB. This part works very 
> well (see code below).
> 
> My problem is the protein has several disulfides defined by CONECT 
> records in the template PDB. The output pdb is missing these records and 
> they are required later.

Modeller does not read CONECT records, but it will write them for any 
disulfide bonds that it knows about. So all you need to do is to patch 
the topology with the disulfides you want. You can either patch them 
explicitly:
https://salilab.org/modeller/10.3/manual/node188.html

or you can have Modeller deduce them from the geometry of your template 
structure:
https://salilab.org/modeller/10.3/manual/node189.html

I think in the latter case, since you already have a suitable alignment, 
adding

mdl.patch_ss_templates(aln)

immediately after your call to mdl.build(), should do the trick.

	Ben Webb, Modeller Caretaker
-- 
modeller-care@ucsf.edu             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage