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