Re: [modeller_usage] Retain residue IDS when mutating and writing PDB

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

On 5/5/20 5:40 PM, Pedro Guillem wrote:
> I'm using Modeller 9.24 to induce a couple of mutations into a PDB.
>
> I noticed that when I execute model.mutate() and export the PDB, the 
> residue indexes are completely different from the original file... ebery 
> residue looses its original position in the sequence and gets renumbered 
> to therever it lands.
>
> Is there a way I can force modeller to stick to the original numbering?

model.mutate() does not change the residue numbering, but likely you are 
doing something else in your script which does (by default Modeller 
numbers everything from 1). You can either renumber manually using 
rename_segments():
https://salilab.org/modeller/9.24/manual/node192.html

or you can transfer residue numbering from another PDB file with 
res_num_from():
https://salilab.org/modeller/9.24/manual/node191.html

See also the "mutate model" script which mutates and handles residue 
numbering:
https://salilab.org/modeller/wiki/Mutate%20model

	Ben Webb, Modeller Caretaker
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