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