Re: [modeller_usage] Treading onto known PDB template

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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