In the last email the "sequence:1hc9: 1 :A:52:B:undefined:undefined:-1.00:-1.00" was a mistake. In practice I'm leaving the sequence to be threaded with no information (:::::::::). I can get it working with one chain, but it fails for more.
>P1;2abx structureX:2abx: 24 :A:52 :B:bungarotoxin:bungarus multicinctus:2.5:-1.00-----------------------YRKMWCDAFCSSRGKVVELGCAATCPSKK----------------------/ -----------------------YRKMWCDAFCSSRGKVVELGCAATCPSKK----------------------*
>P1;1hc9 ::::::::: -----------------------YRKMWCDVFCSSRGKVVELGCAATCPSKK----------------------/ -----------------------YRKMWCDAFCSSRGKVVELGCAATCPSKK----------------------*
On Wed, Jul 8, 2020 at 8:46 AM Geoffrey Woollard < geoff.woollard@mail.utoronto.ca> wrote:
> 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 >> >