What to do when Prompted: assignConnectedResidues only allowed for connected NmrChains

[chb49]

Some background. I currently have two chains in my project and the example I mention below is the my attempt at assigning to the second chain. The first chain can be assigned as normal.

I tried to assign a specific NmrChain (ex. @1579) to a specific residue (Gly 245) by dragging and droopping in the “Sequence Graph” window. It prompted me with the normal prompt shown below, which I pressed “yes”.

Then it prompts me with the following and then it doesn’t assign the residue.

What does this second prompt mean? How do I connect Residues with an NMRchain?

Thanks for your help.

[VickyH]

Hi,

that’s an interesting one. It looks as though making assignments in the Sequence Graph is only allowed from either the default NmrChain @- or from a “connected” NmrChain which has # at the start of its name (e.g. NC:#4).
Connected NmrChains are ones where the where the program knows that the residues are connected with one another (this connecting happens as part of the BB assignment process). If you turn off the peak assignments in the Sequence Graph Settings, then you’ll see that the residues are connected by “bonds”:

It appears you can, however, make the assignment directly in the Edit NmrResidue pop-up. You can get to this by double-clicking on the NmrResidue in the sidebar. We’ve also just the other day added it to the right-hand mouse menu in the Sequence Graph (i.e. right-click on the NmrResidue in the Sequence Graph and go to Edit NmrResidue). Unfortunately, that doesn’t yet seem to be on the update server yet, so I’ll make sure we push that today, as that should make life easier. Once you have the pop-up open, change the NmrChain, Sequence Code and Residue Type and the assignment will be made.
I realise this is considerably less convenient than the dragging in the SequenceGraph, but it should at least allow you to continue working for now.

Overall, though, I’d say it’s a bug that you can’t make assignments from any type of chain in the Sequence Graph. I dare say when the SequenceGraph was originally designed (long before my time) there was some rationale for why it was set up this way. But it doesn’t really make sense to me, and I think we should change the behaviour.

I’ll keep you posted.

Vicky

[VickyH]

Hi,

right-click on an NmrResidue in the Sequence graph will now let you click on Edit NmrResidue.

But we’re only part-way through fixing the other issue.

Vicky

[chb49]

Hi Vicky,

Thank you for your reply and apologize for my slow response.

While I was waiting for a response, I found that I can place my @NC3 nmrchain information into a intermediate nmrchain which is created when doing the “backbone assignment” and then place those into my aminoacid “chain”.

I will also look into trying what you suggested.

In summary, perhaps there was some minor glitch or error in my setup, but I have been able to move foward.

Lastly, thank you for supporting and developing CCPNMR in general. I’ve been a user for 5+ years (starting with 2.4) and have enjoyed it ever since.