Re: [modeller_usage] Treading onto known PDB template
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
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 >
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 >> >
On 7/8/20 5:46 AM, Geoffrey Woollard wrote: > 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.
You can only specify a single residue range in your alignment file, so this will have Modeller read the ATOM/HETATM records from your PDB starting at residue 24 in chain A, until it reaches residue 52 in chain B. If you're not interested in residues 53+ in chain A or 1-23 in chain B, either include the sequence but align it with gaps in the target, or delete the coordinates from the PDB file using a text editor.
Ben Webb, Modeller Caretaker
Ok I see now how I can include all the sequence from the PDB file, and then just put dashes in the alignment in the target. I've been making models of the tetramer and they are making sense by eye.
Now I would like to confirm that I am doing the C4 symmetry right. How does the code below look? I extended it from the link you sent me: https://salilab.org/modeller/9.24/manual/node29.html
Do I need to do all the pairs (AB, AC, AD, BC, BD, CD) or only the minimal (AB, BC, CD)? In other words is the symmetry like the transitive property of equality? Would C3 symmetry between chains ABC be (AB, AC, BC) or just (AB, BC)?
# Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) self.restraints.symmetry.append(symmetry(s1, s3, 1.0)) self.restraints.symmetry.append(symmetry(s1, s4, 1.0)) self.restraints.symmetry.append(symmetry(s2, s3, 1.0)) self.restraints.symmetry.append(symmetry(s2, s4, 1.0)) self.restraints.symmetry.append(symmetry(s3, s4, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0)
On Wed, Jul 8, 2020 at 4:05 PM Modeller Caretaker modeller-care@salilab.org wrote:
> On 7/8/20 5:46 AM, Geoffrey Woollard wrote: > > 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. > > You can only specify a single residue range in your alignment file, so > this will have Modeller read the ATOM/HETATM records from your PDB > starting at residue 24 in chain A, until it reaches residue 52 in chain > B. If you're not interested in residues 53+ in chain A or 1-23 in chain > B, either include the sequence but align it with gaps in the target, or > delete the coordinates from the PDB file using a text editor. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
On 7/17/20 5:56 AM, Geoffrey Woollard wrote: > Do I need to do all the pairs (AB, AC, AD, BC, BD, CD) or only the > minimal (AB, BC, CD)? In other words is the symmetry like the transitive > property of equality? Would C3 symmetry between chains ABC be (AB, AC, > BC) or just (AB, BC)?
It is a restraint, so if you restrain A to be like B and A to be like C you do not need to restrain B to be like C.
Ben Webb, Modeller Caretaker
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