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Editor: damberger
Time: 2014/11/08 00:48:00 GMT+1 |
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Note: |
changed: - f. Your WriteAssignment.lua dialog should look something like "this":StructureCalculationsOfComplexesWriteAssignmentSettings f. Your !WriteAssignment.lua dialog should look something like "this":StructureCalculationsOfComplexesWriteAssignmentSettings
Determining the structures of complexes or oligomers requires some additional procedures. Typically isotope-labeling of individual components helps to simplify the problem. The project is therefore divided into subprojects where only the resonance assignments of the isotope-labeled component are determined. Later the assignments of the individual components must be merged so that the NOEs between components can be analysed using experiments which use isotope-filtering and -editing to obtain only intermolecular NOEs.
CARA provides support for this analysis by allowing the definition of samples with different isotope-labeling patterns Moreover, SpinLinks? which represent NOEs? between spins can be defined to only appear in a subset of NOESY spectra. Via the SpinLink? visibility the subset of NOEs? visible in isotope-filtered/edited experiments can be represented. (See release notes for how to do this, further information is forthcoming on the wiki).
a. SequenceTable?: renumber Chain of protein B starting with a number that is +1 relative to the maximum residue number of protein A in project A. Right-click on the first residue of protein B and select "renumber from here" entering the starting ChainNr?. (158 in the example shown here).
b. Load the version 11 or later of WriteAssignments.lua into the repository containing Project B.
a. Select Project ProteinB
b. checkbox number by ChainId
c. Enter a number in the "Add offset to SpinId?" field that is larger than the maximum SpinId? determined in step 4 (e.g. 5000)
d. Select format CYANA.
e. Click OK (this writes out a sequence file starting at the ChainNr? of the first residue of protein B, and a chemical shift list .prot where each spin has an Id in the output file which is +5000 compared to the Id it has in Project B. We do this so that the sequence and chemical shift list can be merged with that of project A.
f. Your WriteAssignment.lua dialog should look something like this
a. In the projects SequenceExplorer? assign the sequence of protein A the chain identifier A (right-click "set chain" and enter "A").
b. Append the Sequence of protein B: right-click Append Chain, select the sequence file of protein B generated in step 5, and assign the ChainId? "B".
c. read in the chemical shift list of protein B: right-click on the project ProteinAandB and "Import-Atom List" selecting the option AtomList? references "Residues"