[modeller_usage] Re: Modeller is transforming ZN2 atom names to ZN
To:
Subject: [modeller_usage] Re: Modeller is transforming ZN2 atom names to ZN
From: Pedro Guillem <>
Date: Mon, 27 Feb 2023 21:04:18 +0100
Awesome Ben, thank you so much for your reply!!!
As long as the atom name is the same it will be fine.
I just modified restyp.lib like you suggested but the output PDB is still
generated with ZN only.
I also deactivated/activated the conda environment (where modeller is
installed). I tried both env.io.heatatm True and False.
ORIGINAL:
ATOM 599 ZN ZN2 A 74 28.353 -59.777 92.760 1.00 0.00
ZN
ATOM 600 ZN ZN0 A 75 40.834 -53.893 90.903 1.00 0.00
ZN
ATOM 601 ZN ZN2 A 76 26.392 -65.030 97.280 1.00 0.00
ZN
POST-MODELLER:
HETATM 600 ZN ZN A 74 28.353 -59.777 92.760 1.00 0.00
ZN
ATOM 601 ZN ZN0 A 75 40.834 -53.893 90.903 1.00 0.00
ZN
TER 602 ZN0 A 75
HETATM 603 ZN ZN A 76 26.392 -65.030 97.280 1.00 0.00
ZN
Any hints?
Pedro
El lun, 27 feb 2023 a las 20:24, Modeller Caretaker (<
>) escribió:
> On 2/27/23 10:22 AM, Pedro Guillem via modeller_usage wrote:
> > I'm using modeller to mutate a single residue in a PDB template that
> > contains ZN atoms.
> >
> > The mutation is taking place correctly, but the resulting PDB is written
> > with the name ZN instead of ZN2, which is in the original template. My
> > ZN is in a different coordination state and I need the name to stay
> > ZN2 in the mutated structure.
>
> Yes, Modeller treats the ZN2 residue type as a synonym for ZN. This is
> defined in the modlib/restyp.lib file in your Modeller distribution. If
> you like, you can modify this file to remove the synonym, i.e. find the
> line
>
> HETATM | ZN ZN2 | z | | ZN2 | zinc, +2
>
> and replace with
>
> HETATM | ZN | z | | ZN2 | zinc, +2
>
> Modeller will then treat ZN and ZN2 as two different residue types.
> Since it then won't recognize ZN2, it will treat it as a rigid body,
> which is probably fine for your application, although you could add a
> new ZN2-specific residue type if you want as per
> https://salilab.org/modeller/FAQ.html#8
>
> Ben Webb, Modeller Caretaker
> --
> https://salilab.org/modeller/
> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
>
Awesome Ben, thank you so much for your reply!!!
As long as the atom name is the same it will be fine.
I just modified restyp.lib like you suggested but the output PDB is still generated with ZN only.
I also deactivated/activated the conda environment (where modeller is installed). I tried both env.io.heatatm True and False.
ORIGINAL:
ATOM Â Â 599 Â ZN Â ZN2 A Â 74 Â Â Â 28.353 -59.777 Â 92.760 Â 1.00 Â 0.00 Â Â Â Â Â ZN Â ATOM Â Â 600 Â ZN Â ZN0 A Â 75 Â Â Â 40.834 -53.893 Â 90.903 Â 1.00 Â 0.00 Â Â Â Â Â ZN Â ATOM Â Â 601 Â ZN Â ZN2 A Â 76 Â Â Â 26.392 -65.030 Â 97.280 Â 1.00 Â 0.00 Â Â Â Â Â ZNÂ Â
POST-MODELLER:
HETATM Â 600 ZN Â Â ZNÂ A Â 74 Â Â Â 28.353 -59.777 Â 92.760 Â 1.00 Â 0.00 Â Â Â Â Â ZN ATOMÂ Â Â 601 ZN Â ZN0 A Â 75 Â Â Â 40.834 -53.893 Â 90.903 Â 1.00 Â 0.00 Â Â Â Â Â ZN TERÂ Â Â Â Â 602 ZN0 A Â 75 HETATM Â 603 ZN Â Â ZNÂ A Â 76 Â Â Â 26.392 -65.030 Â 97.280 Â 1.00 Â 0.00 Â Â Â Â Â ZN
Any hints? Pedro
El lun, 27 feb 2023 a las 20:24, Modeller Caretaker (<">>) escribió:
On 2/27/23 10:22 AM, Pedro Guillem via modeller_usage wrote:
> I'm using modeller to mutate a single residue in a PDB template that
> contains ZN atoms.
>
> The mutation is taking place correctly, but the resulting PDB is written
> with the name ZN instead of ZN2, which is in the original template. My
> ZN is in a different coordination state and I need the name to stay
> ZN2Â in the mutated structure.
Yes, Modeller treats the ZN2 residue type as a synonym for ZN. This is
defined in the modlib/restyp.lib file in your Modeller distribution. If
you like, you can modify this file to remove the synonym, i.e. find the line
HETATM | ZN ZN2Â Â Â Â Â Â Â | z |Â Â | ZN2Â | zinc, +2
and replace with
HETATM | ZNÂ Â Â Â Â Â Â Â Â | z |Â Â | ZN2Â | zinc, +2
Modeller will then treat ZN and ZN2 as two different residue types.
Since it then won't recognize ZN2, it will treat it as a rigid body,
which is probably fine for your application, although you could add a
new ZN2-specific residue type if you want as per https://salilab.org/modeller/FAQ.html#8