Hello Ben thank you for your kind update:).
No I have taken this into account i.e. starting residue is 2 accordingly my starting missing residue is 89 so I made it 88.
Please let me know at least then which of the above I should be using for an oligomer meaning should i designate each chain? (I will take care of the rest of the analysis to manage your time.)
Thanks Ben:) Joel
On Sat, Sep 24, 2022 at 12:00 AM Modeller Caretaker < firstname.lastname@example.org> wrote:
> On 9/23/22 4:52 AM, Joel Subach via modeller_usage wrote: > > Hello, for the above topic I have a heptamer, accordingly should my > > missing residue > > code for chains A-G be just and A-chain indication with the B-G being > > modeled via default or should I designate each chain, see below: > > > > return Selection(self.residue_range(`88:A´, `100:A´)) > > This will just refine the loop in the A chain. > > > return Selection(self.residue_range('88:A', '100:A'), > > self.residue_range('88:B', '100:B'), > > self.residue_range('88:C', '100:C'), > > self.residue_range('88:D', '100:D'), > > self.residue_range('88:E', '100:E'), > > self.residue_range('88:F', '100:F'), > > self.residue_range('88:G', '100:G')) > > > > I tried the later (A-G coding) and received the below error where there > > should be this missing residue? > > * > > * > > *raise KeyError("No such %s: %s" % (indxtyp, indx)) > > * > > *KeyError: 'No such residue: 88:B'* > > You are probably assuming that Modeller numbers the residues in each > chain starting from 1. It doesn't by default, although you can ask it to > do so: > https://salilab.org/modeller/10.3/manual/node30.html > > Ben Webb, Modeller Caretaker > -- > email@example.com https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > >