Hello,
Tim says:
Really a single molecular system should be used for both components of the
complex. The whole idea behind a molecular system is to represent a
complex or sample. Hence the residue ranges are configured for each
molecular system separately and you only get mixing of chains within a
system (by the data model definition), so the GUI reflects this.
The initial problem was probably the molecular setup, where Analysis
should probably be clearer about the role of the mol systems vs chains
(improving in v3).
Here, the solution is to move chain B to MS1. Do this via Molecules:
Molecules|Chains - Select "Mol System for new chain" as MS1 and the
"Template for new chain" as the peptide. Once the new chain B is made
Assignment:Copy Assignments|Between Molecule Chains, going from MS2:B to
MS1:B.
Wayne
On Wed, 20 Apr 2011, Fowler, Andrew wrote:
> I've searched the archives and this was sort of asked about a year ago, but I
> didn't see any resolution…
>
> I'm at the point where I'm trying to make distance restraints in preparation for
> structure calculations, probably using Aria. I have a protein/peptide complex
> where the protein is in MS1/chain A (13C/15N labeled) and the peptide is in
> MS2/chain B (unlabeled).
>
> in M:Structure:Make Distance Restraints:Residue Ranges, the only option that's
> available to me in the Chain column is A, regardless of the peak list I've
> selected. Depending on the particular spectrum/peak list, some dimensions should
> be B or A+B. I've tried adding a residue range, but that doesn't help. In
> M:Experiment:Experiments, the corresponding NOESY spectra are defined to apply
> to both MS1 and MS2, with intramolecular experiments assigned appropriately.
>
> Only somewhat related, does anyone have any suggestions for adding calcium ions
> and defining how they're "connected" to the protein? I suppose I can always do
> this later in my calculations after I have a rough structure.
>
> --
> Dr. Andrew Fowler | University of Iowa
> Associate Director | B291 Carver Biomedical Research Building
> Medical NMR Facility | Iowa City, IA 52242
> 319-384-2937 (office) | 319-335-7273 (fax)
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