Create and edit an experiment prototype

The Experiment prototypes can be edited through M: Experiment: Experiment Prototypes. The existing prototypes in the {Prototypes} tab are normally not editable as these are reference information and should be edited only centrally.

Adding new prototypes and new reference experiments are therefore more likely to be useful. Ultimately it is the responsibility of anyone who adds reference information to understand what he/she is doing. The explanation here is therefore focused on the simplest way to proceed:

• • Start in the {Prototypes} tab.

    • If there is a closely similar experiment prototype, it makes sense to use it as a starting point. It is at a later stage simple to change atom names, parameters etc., and to remove atom sites. To edit in an already existing experiment type. Select this as a template experiment and press [Create Copy].

      • Then edit the copy, starting with the columns |Name|, |Category|, |Synonym|, and |Keywords| in the {Prototypes} tab and continue on the other tabs. The numerical columns can be left alone, as values in those columns will adjust to changes made in the other tabs. Remember later in the {Ref Experiments} tab to rename and remove or add reference experiments to fit.

    • If the experiment prototype is unique, or far from similar to the other experiment prototypes, it might be best to start from scratch. To create a new prototype click [Create New].

      • Then set the |Name|, |Category|, |Synonym|, and |Keywords| columns, ignoring the rest of the columns on this tab. Try to make sure you have got the nomenclature right, and that the name does not duplicate that of any other existing prototype.

  • Go to the {Atoms & Measurements} tab to add/modify information in the ‘Atom Sites’ and the ‘Exp Measurements’ tables:

• • • To add a new atom site in the ‘Atom Sites’ table, select the one in the pulldown menu besides the [Create new type] button and press the button.

    • To create an experiment measurement to an atom site (if you e.g. want to measure the shift), click the [Create New] button under the ‘Exp Measurements’ table while the atom site is selected. If the atom site was not simultaneously selected while clicking [Create New] it is possible to set the related atom site by editing in the table under |Atom Site|.

• • Go to the {Exp Graphs} tab:

• • • To create a new experiment graph in the top left table, click [Create New] under the ‘ExpGraphs’ table. Note: You will need more than one experiment graph if you have several distinct magnetisation transfer flows in your experiment.

    • Add experiment transfers by clicking [Create New] at the bottom of the ‘ExpTransfers’ table. Edit the fields in the table to get the contents right.

    • Add experiment steps by clicking [Create New] under the ExpSteps Column. Edit the fields in the table to get the contents. Note that this table must follow the magnetisation transfer step by step. E.g. an HSQC experiment would have steps in order of: ‘1 Shift(H); 2 Shift (N); 1 Shift (H)’ (see Figure above).

• • Go to the {Ref Experiments} tab to add reference experiments:

• • • It is easiest to start by first creating the reference experiment with the highest dimensionality (specified under |numDims|). Note: There should always be a reference experiment with the maximum dimensionality of the prototype, and with the same name as the prototype.

    • Add a new reference experiment dimension for every dimension in the reference experiment by selecting the reference experiment and clicking [New RefExpDim] under the ‘RefExpDimRefs’ table. Edit in the ‘RefExpDimRefs’ table if needed. Note: Add dimensions in order of the magnetisation flow; the mapping to actual dimensions is done elsewhere. In most cases the only column you may need to change is |expMeasurement|.

    • Create the other reference experiments. It is good practice to have a reference experiment for all combinations of axes that people might sensibly choose to measure, even if they are not very likely. That means taking most combinations, but avoiding eg. ‘H[N[ca]]’ (useless), ‘hnCAHA’ (useless) and h[N[CA]] (technically impossible). First select the highest-dimensionality reference experiment in the top table and click [Create Copy]. Change the name so that one or more atom sites are in lower rather than upper case, as a sign that these are not measured. Now select the corresponding dimensions in the lower table and press [Delete RefExpDim]. This will give you a correct reference experiment with lower dimensionality, provided the highest-dimensionality reference experiment was correct. Most experiments can be reversed; the exceptions are out-and-back experiments like H[n[CA]], or symmetric experiments like H[C]_H[C].NOESY. For reversible experiments you should make a further copy of your highest-dimensionality reference experiment. Now change the name of the copy so that the atom sites are in the opposite order (e.g. from HNCAHA to HACANH) and set the |isReversed| column to Yes. Make copies of the highest-dimensionality reverse reference experiment, and use them to create lower dimensionality reversed reference experiments like you already did for the non-reversed case.

    • Add any information you may have for the |Synonym| or |Systematic Name| columns of each individual reference experiment.

Note: Experiment prototypes and reference experiments are editable when created, but become frozen when the project has been closed and they are reloaded from disk. If you really need to edit these data after the initial creation (remember, this is reference information, and changing data that is used in actual projects may introduce errors) do as follows: Go to the command line, and get hold of the MemopsRoot object (you can get it as top.project). Then select the NmrExpPrototype you want to edit, and set myNmrExpPrototype.isEditable = True. Do the same for existing RefExperiments you want to modify.

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