Re: [modeller_usage] Modeling loop using template from PDB file

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

On 12/6/16 3:54 PM, Markus Heller wrote:
> I have a structure (A) which is missing a stretch of a dozen or so
> residues.  I also have the structure of the protein from a different
> organism which has said stretch of residues resolved (B).  Now I'd
> like to take the coordinates of A and model the missing residues
> using the relevant coordinates (i.e. for these residues only) from
> B.
>
> How would I go about doing this?

Just make an alignment containing both proteins A and B, and align the 
missing region with B and the rest with A, as per
https://salilab.org/modeller/FAQ.html#1

If you're happy with the A coordinates and don't want them to move at 
all, select only the B region in select_atoms():
https://salilab.org/modeller/9.17/manual/node23.html

	Ben Webb, Modeller Caretaker
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