Discussion group for the ARIA software

[Mohammad Rafid Feisal <rafidfei AT ualberta.ca>]

Hi Benjamin, 

Regarding Leu 81, 

Since you mentioned, the assignment should be {81.HD2#} for the H dimension, what about the C dimension? Technically, you can't differentiate between CD1 and CD2 for leucines. 

Shouldn't it be {81.HD#} indicating it can HD11,12,13 or 21,22,23 followed by {CD#} indicating it can be CD1 or CD2? 

The same can assumed for Val CG1/2 and HG11/21?

Correct me if I'm wrong. Can I add wildcard entries for the carbon dimension? Or should I stick to HD1# and HD2#? 

Thank you. 

Regards, 

Rafid Feisal

On Tue, Feb 6, 2024 at 2:17 AM Benjamin Bardiaux <aria-discuss AT services.cnrs.fr> wrote:

Hi Rafid,
The conversion tool of ARIA(web) supports wildcards in the NMRView peak files for ambiguous assignments.
In the case you shown, the assignment would then be {81.HD2#} for the H dimension.

Best,

Benjamin

On 02/02/2024 01:50, "Rafid Feisal" (via aria-discuss Mailing List) wrote:
> Hi,
>
> It seems ARIA deals with pseudoatom assignments differently when I set it up
> on the spectrum list with "use assignments" vs when I DON'T select "use
> assignments". Here's a comparison of the output files generated after ARIA
> runs without and with "use assignments" functions. I am using NMRViewJ for
> analyzing my spectra and assigning my peaks.
> All of it is referring to peak 784:
>
> Without "use assignments":
>
> noe_restraints.assignments:
> ref_spec: hcnoesy_R14_pureauto_jan31_2024, ref_peak: 784, id: 612, d: 1.99, u:
> 3.06, u_viol: 0.00, %_viol: 0.0, viol: no, reliable: no, a_type: S
>        ILE78   HA      -   LEU81 HD11         d: 2.14 +/- 0.55, weight: 1.0
>        ILE78   HA      -   LEU81 HD12
>        ILE78   HA      -   LEU81 HD13
>
> The respective unambig.tbl shows:
> assign (segid "    " and resid   78 and name   HA) (segid "    " and resid
> 81 and name HD12) 2.359 0.696 0.696 weight 1.000 ! spec=hcno...2024, no=784,
> id=612, vol=1.783746e+00
>      or (segid "    " and resid   78 and name   HA) (segid "    " and resid
> 81 and name HD11)
>      or (segid "    " and resid   78 and name   HA) (segid "    " and resid
> 81 and name HD13)
>
> It can provide a proper restraint with the respective pseudoatoms as it should
> be.
>
> With "use assignments: I have assigned it to LEU81 HD22
> ref_spec: hcnoesy_jan25_2024, ref_peak: 784, id: 615, d: 2.76, u: 3.18,
> u_viol: 0.05, %_viol: 0.0, viol: no, reliable: no, a_type: M
>        ILE78   HA      -   LEU81 HD22         d: 2.68 +/- 0.49, weight: 1.0
>
> Shouldn't it be?:
>        ILE78   HA      -   LEU81 HD22       d: 2.14 +/- 0.55, weight: 1.0
>        ILE78   HA      -   LEU81 HD21
>        ILE78   HA      -   LEU81 HD23
>
> Subsequent unambig.tbl shows:
> assign (segid "    " and resid   78 and name   HA) (segid "    " and resid
> 81 and name HD21) 2.435 0.741 0.741 weight 1.000 ! spec=hcno...2024, no=784,
> id=615, vol=1.783746e+00
>
> It doesn't provide other atoms in the list with the OR function as a
> restraint, as it should have HD22, 21, and 23.
>
> Could anyone kindly help me out with this? I might be unaware of certain
> settings I need to make on NMRViewJ and/or ARIA. All these structure
> calculations were done on ARIA Web.
>
> Thank you.
>
> Kind regards,
> Rafid Feisal

--
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Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Bacterial Transmembrane Systems Unit (BaTS)
CNRS UMR 3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
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