On 3/15/10 2:15 AM, wayj86 wayj86 wrote: > I am trying to fix a protein with 6 missing aa. This protein has a resid > from 500 to 650, with three HETATM residues (N-glycan) from 800 to 802 > (discontinuous with the protein resnumber). Here is my script to run > modeller: ... > By running this script I did got a model with missing residues fixed and > HETATM keeping, but the chain ID was blank (because only one chain was > built), and the resnumber was from 1 to 154. I did hope to keep the > original chain ID and the resnum, so I try the rename_segments, like: ... > Now in the final model y.ini the chain ID was defined as "A", and resnum > was from 500 to 650. However, the HETATM residues was from 651 to 653, > but not 800 to 802. So should I modify my scripts to fix the protein and > keeping its original chain ID, resnumber and HETATM residues? Thank you > very much for your attention.
rename_segments renumbers residues sequentially. It is the simplest of the methods for renumbering residues detailed at http://salilab.org/archives/modeller_usage/2009/msg00245.html
If you want to have non-sequential residue numbering, you can assign numbers to each residue individually.
Ben Webb, Modeller Caretaker