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Re: [modeller_usage] Could modeller change query position in result pdb file?



On 2/20/19 6:23 AM, jb ZHOU wrote:
    I used Modeller to model a sequence in UniProt (UniProt Accesion: Q04721), and I only used parts of sequence to model (from 414 to 532),  and I want to get the final three-dimensional structures file (pdb file) which the first amino acid number still start with 414 and the last amino acid number is 532. But in fact the first amino acid number in the final pdb file start with 1 (see figure below, GLU's position is 1, but it is 414 in UniProt,).

    I could write a script to map it manually, but it is very inconvenience, so could modeller (or  module  in modeller) realize this ?

Of course. Override special_patches() and have it call rename_segments() to renumber the residues. See
https://salilab.org/modeller/9.21/manual/node30.html

	Ben Webb, Modeller Caretaker
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