Dear Sylwia,
I think making a new molecule or chain is not such a good idea, because this will interfere later on with several things. What I would do is to just make assign the second set of peaks from this two residues to two new spin systems. This is probably how I would do this, but there are several ways.
1) Just make a normal spin system like you would normally do (for instance click on an intra-residual peak go to the assign popup and make <New> resonances and click on 'Set same spin system' and go on filling the spin system with resonances by going to other peaks and assign them to this spin system and setting atom types etc. The usual).
2. At some point when you finished filling up the spin system click on Assign and assign it to the residue you want. Analysis will the ask you 'There is an existing 231 Ala spin system Ok to merge' you just say NO. Now you have two 231 Ala spin systems.
When I do it in this way I see two entries in my Chemical Shifts Table and also when looking at the 'Residue Information' for instance it gives me both shifts. I think a new chain is more meant for two actual different chain in a homodimer, since that is what the API information says: http://www2.ccpn.ac.uk/api-documentation/ccpnmr/ccpnmr2.2/python/ccp/api/doc/molecule/MolSystem/Chain/index.html Therefor I see this give less problems with for instance making distance restraints later on, since now you have just two sets of resonances connecting to the same set of atoms in the molecule instead of to different atoms in different chains.
As said this is what I would do, but I am curious to see what other people have to say about this.
best regards,
Joren
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