Re: [modeller_usage] Treading onto known PDB template

To: Modeller Caretaker <>

Subject: Re: [modeller_usage] Treading onto known PDB template

From: Geoffrey Woollard <>

Date: Wed, 8 Jul 2020 08:46:55 -0400

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Cc:

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 <">> 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
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