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