Dear Modeller creators,
Hello, Modeller is one of state-of-the-art homology modeling software and I have already used several years to model three-dimensional structures.
Recently, I have a question about modeller result file (pdb file). I would like to use an example to illustrate my question.
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 ?
Sincerely,
Zhoujb
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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jb ZHOU -
Modeller Caretaker