OK great this helps a lot.
Using the example https://salilab.org/modeller/9.24/manual/node29.html, let's say I just want to model a subsequence in the middle (YRKMWCDAFCSSRGKVVELGCAATCPSKK, residues 24-52). How would I change the ali file. I'm getting stuck on the "structureX:2abx: 24 :A:52 :B" part since really it's 24-52 in chain A and 24-52 in chain B, not 24 in chain A to 52 in chain B.
I'm doing something similar, except "YRKMWCDAFCSSRGKVVELGCAATCPSKK" is much longer with some gaps in it.
C; example for building multi-chain protein models
>P1;2abx structureX:2abx: 24 :A:52 :B:bungarotoxin:bungarus multicinctus:2.5:-1.00-----------------------YRKMWCDAFCSSRGKVVELGCAATCPSKK----------------------/ -----------------------YRKMWCDAFCSSRGKVVELGCAATCPSKK----------------------*
>P1;1hc9 sequence:1hc9: 1 :A:52:B:undefined:undefined:-1.00:-1.00 -----------------------YRKMWCDVFCSSRGKVVELGCAATCPSKK----------------------/ -----------------------YRKMWCDAFCSSRGKVVELGCAATCPSKK----------------------*
On Mon, Jul 6, 2020 at 7:32 PM Modeller Caretaker modeller-care@salilab.org wrote:
> On 7/6/20 2:49 PM, Geoffrey Woollard wrote: > > Can I do the modelling in the context of the tetramer? Otherwise I would > > have to just do it with the protomer, and then delete out parts that > > were clashing. > > > > Are there options for applying symmetry during modelling? > > Sure, this is also covered in the manual: > https://salilab.org/modeller/9.24/manual/node29.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >