Change Molecule Sequence

How to change the sequence of an existing chain that already has assignments.

This is a little complicated. You can not change the sequence in place, since Labelled Molecules, Sample descriptions and some other things assume the existing sequence. You will have to make a new chain with the new sequence and transfer your assignments. If you have sample descriptions or labelled molecules in your project (most people do not) you will have to fix them up afterwards.

This is the procedure:

First make the new molecule and chain:

• • M:Molecule:Molecules{Sequences}

    • Select starting chain and press [Copy Sequence]. This will bring you to:

    • {Add Sequence}.

    • Edit the sequence to get the one you want, and press [Add Sequence],

    • giving a suitable name (e.g. 'ModifMol').

• • • Go to {chains}

• • • • Select target MolSystem (likely the one you started from)

      • Select new molecule: ModifMol

      • Press [Make Chain From Template], and name it e.g. B

Then transfer assignments:

• • M:Assignment:Copy Assignment {Between Molecule Chains}

    • Set source to original chain

    • Set target to new chain

    • Set all experiments to "Move to Target"

    • Check the automatic sequence alignment in the bottom table and make sure it is correct

      • NB the routine will only work where the residue type is the same in both sequences.

      • If you are mapping between different types, set the target residue to None.

• • • Press [Copy Assignments!]

    • Make a note of residues where there are still 'Source resonances' left - these were incompletely copied

    • If there are none of those you should be done

Now check the results and fix any remaining resonance by hand:

• • M:Peak:Draw Parameters{Annotation Style}: Set 'Chain Assignments' to On and press [Update Full Annotations]

  • This lets you see the chain for all resonances (you can undo it afterwards).

  • Look in M:Molecule:Atom Browser or an overview of what is assigned in which chains.

  • M:Resonance:Resonances for manual assignments

• • • Sort by residue (now includes chain code) to find resonances that have not been moved over.

    • Residues that map to a different type (e.g. an Ala to a Thr) must be reassigned by hand

      • Select one resonance, and reassign it to the right target

        • Say YES when asked if you mean it

        • Say YES when asked if you want to reassign other resonances in the same spin system

      • Check the result; resonances that do not matchin the two residue types will not be assigned correctly. Assign those by hand.

    • Resonances that have no equivalent in the new molecule must be deassigned, and peaks possible reassigned to something else.

    • Here it depends on what you want to do.

      • If you want ot keep the spin system but deassign if from the chain (e.g. an impurity) go to

      • M:Resonances:Spin Systems and deassign the spin system as a whole

      • If you want to reassign the peaks, select the resonance in M:Resonance:Resonances, press [Show all peaks], and take it from there

      • If you want to deassign individual resonances, click [Deassign] and [Remove from Spin System] in M:Resonance:Resonances

Finally delete the original chain and molecule:

• • Go to M:Molecule:Molecules{Chains} and delete the old chain

  • Say yes when asked whether to delete the molecule also - the question is cryptic, but that is what it means.

You are done.