I performed this task enough to write a small script to do this for me. The
code is on the wiki (http://www.pymolwiki.org/index.php/Zero_residues).
It's easy to use. Just issue
zero_residues proteinName
to renumber protein name to start at 0. Or write
zero_residues proteinName, 10
to renumber the residues such that the first is 10.
HTH,
-- Jason
> Message: 5
> Date: Fri, 4 May 2007 08:56:07 +0200
> From: "Golynskiy, M.V." <[email protected]>
> Subject: [PyMOL] automatic renumbering of proteins?
> To: <[email protected]>
> Message-ID:
> <[email protected]>
> Content-Type: text/plain; charset="us-ascii"
>
> So I'm trying to make a .pml script where I generate "rotamers" of
> protein A around protein B using "rotate axis, degree, object" and
> creating new object of rotated protein A - this generates a number of
> rotamers, but they basically form a sphere until you align them, and so,
>
>
> the last step is that I align all the rotamers I've generated either on
> N- or C- term of protein A (i.e. the Ca atom of first/last residue),
> depending on my choosing
>
>
>
> So, at the moment, I manually renumbering whatever protein I'm
> generating the rotamers for and setting it to some obscure number (like
> 5000) that is unlikely to be used by most pdb files
>
>
>
> Manually, I do this by using
>
> alter structure1, resi=str(int(resi) + 4999) ; rebuild
>
>
>
> - this takes the object structure1, which starts at 1 as the
> first amino acid residue and changes it to be 5000, so in case of my
> alignments, aligning my rotamers with structure1 doesn't accidentally
> align any other object in the pdb file...
>
>
>
> doing this manually is a pain, especially since a number of pdb files
> don't start with residue number 1 and I have to keep manually
> renumbering the proteins...
>
>
>
> is there a way to easily set the first residue to be 5000 or last
> residue to be 5000? Regardless of what the object?
>
>
>
> for example to do the following (i.e. what code might I use to do the
> following)
>
> create object, sele
>
> if the first residue number in object is not numbered "1", get value of
> first residue number , calculate the difference between 5000 and value
> of first residue number and add that difference to all residue numbers?
> i.e. if my peptide starts at residue 23 and I want that to be 5000...
>
>
>
> Similarly, if the last residue number of the object is not 5000, get
> value of last residue number, calculate the difference between 5000 and
> the value of last residue number and add/subtract this difference to all
> residue numbers? i.e. if my peptide ends on residue 38 and I want that
> residue to be 5000
>
>
>
> I'd like this to be a "general" code, so that I can renumber and object,
> regardless of whether the first residue is numbered 3, 600 or 2100, etc
>
> Anyone familiar with how to do this?
>
> I would greatly appreciate it
>
> Thanks,
>
> m
> --
Jason Vertrees ([email protected])
Doctoral Candidate
Biophysical, Structural & Computational Biology Program
University of Texas Medical Branch
Galveston, Texas
http://www.best.utmb.edu/
http://www.pymolwiki.org/
