Subject: Re: [modeller_usage] POSITION IONS IN MODELS
From: Modeller Caretaker <>
Date: Thu, 11 Dec 2008 14:24:31 -0800
Cc:
Lella Sana wrote:
> I have a problem with adding Calcium ions in my models.
> I'm using this TOP script:
...
> The models generated by MODELLER contain the ions:
> ATOM 603 OXT GLU 85 14.608 -30.221 -12.881 1.00 30.85 1SG 604
> TER 603 GLU 85 1SG 605
> HETATM 604 CAL CAL 86 22.805 -57.972 -18.845 1.00 0.00 1SG 606
> HETATM 605 CAL CAL 87 -43.926-115.000-182.203 1.00 0.00 1SG 607
> END
>
> But the position of these Calcium ions is completely wrong, outside
> of the molecule and differing from the template. How can I solve this
> problem?
Your script and alignment look OK to me. My best guess is that you're
using an old version of Modeller with a new template PDB file (post
remediation). (The post-remediation calcium ion is called "CA" but old
versions of Modeller called it "CAL".) Modeller will only inherit
coordinates from templates if the atom names match. Does your PDB file
call the calcium atoms "CA" or "CAL" ? If "CA" (which is what it should
be these days) the best solution is to upgrade Modeller to the latest
release, 9v5, which uses remediated residue and atom names. If for some
reason you can't do that, you can either change your alignment to use
'.' rather than '3', since BLK residues work just fine for ions and
don't care about atom names, or you could possibly rename the calcium
atoms and residues in your template PDB to "CAL".
Ben Webb, Modeller Caretaker
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