Hello,
Tim says:
Under normal circumstances each spectrum will be associated with only one
molecular system; there was only one sample and the molecular system
generally reflects what's in the sample. So I would suggest checking the
Mol Systems column of the main Experiments table and making sure that each
experiment is associated with only the correct molecular system. If two
molecular systems are selected then Analysis will think that both are
possible.
The molecular system setting for an experiment is added the first time you
assign a peak to an atom within that system, so that it knows what to use
in future. If there is a bogus molecular system association it is
frequently due to a bogus assignment to an atom within that system.
The coordinate warnings are simply because a structure doesn't (totally)
match the molecule being assigned. The coordinates are fetched via the
atom for an assignment and there is a very tight link between the
molecular system atom (the one assigned to) and the atom in the structure.
Hence, it is unlikely that the wrong structure object is being inspected
per se, but rather that the contents of the structure object are wrong.
Could it be that when a PDB file was loaded the wrong molecular system was
selected? When you load a structure into an existing setup, you have to
select a mol system to say what it is the structure of (as far as the NMR
goes). We do allow truncations though, in case you don't have the whole
structure, but naturally this leads to absent coordinates.
Wayne
On Sat, 12 Mar 2011, Tozawa, Kaeko wrote:
> Hello there,
>
> I have two molecular systems in a project, MS1 and MS2. They are different molecules.
> When I try to assign a peak of the molecule of MS2 and click right mouse button on a peak and go to Assignment:Assignment Panel, even if I've already assigned F1 and F2 dimensions as MS2 atoms, sometimes it gives assignment possibilities of F3 both MS1 and MS2. And I've got loads of lines of warnings like;
>
> Couldn't find coordinate residue Asp 52
> Couldn't find coordinate residue Lys 70 HE2
> etc.....
>
> because the molecule for MS1 has 100 residues but MS2 is much smaller but apparently analysis tries to find nonexistent atoms based on the MS1. Strangely, this behaviour does not consistently happen and most of the times it gives only MS2 possibilities once I assign the other dimensions as MS2.
>
> I'm not sure if I switch on/off something unintentionally. Do you have any idea what's going on here?
>
> Thank you.
>
> Kaeko
|