Discussion group for the ARIA software

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

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