But for future PDB deposition (I guess that's the ultimate purpose of the
exercise), wouldn't it be better to leave the residue numbering as it is (i.e.
in reference to the location on the sequence)?
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[email protected]] On Behalf Of Pavel Afonine
[[email protected]]
Sent: Monday, April 25, 2011 8:14 PM
To: [email protected]
Subject: Re: [ccp4bb] renumbering amino acid residues in a pdb file
Hi Michael,
another option:
phenix.pdbtools fab.pdb renumber_residues=true
that will re-number residues in all chains.
Pavel.
On Mon, Apr 25, 2011 at 9:50 AM, Michael Murphy
<[email protected]<mailto:[email protected]>> wrote:
Hi All,
I have a pdb file of a single domain from a protein. The amino acid
residues are numbered based on their position in the full length protein, so
they do not start at 1, but I would like them to. Coot has a Renumber Residues
feature under the Calculate menu, but it does not appear to work at all. For
example, I want to renumber chain B, which starts at 445 and goes up to residue
522, to start at 1. So I open Renumber Residues, select chain B, enter the
residue range 445 to 522, then the offset of -444. Coot does not make the
change. Is there something else that I should be doing here?
Thanks
