Re: [modeller_usage] How should I fill in the missing rsidues with the same chain id, resnumber and HETATM keeping?

[Modeller Caretaker <>]

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
--
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