Experiment: Experiment Prototypes

View and Edit NMR Experiment Prototypes

NmrExpPrototypes describe NMR experiments: The magnetisation transfer flow, what is being measured, and how the nuclei on the different axes are connected. The NmrExpPrototype groups a series of RefExperiments that share a magnetisation transfer pathway but can have different dimension and axis selection.

Finding an experiment description

NmrExpPrototypes and RefExperiments names are complex, but follow a systematic nomenclature; understanding what they mean and what your target experiment should be called is a great help. A detailed explanation can be found on the documentation Wiki under ‘Core Concepts -> NMR Experiment Nomenclature’, or (somewhat out of date) at http://www.springerlink.com/content/h57q76k245r14558/

The best approach is to zoom in on a limited set of candidates and check the names and the detailed descriptions. Sorting on the ‘Name’, ‘Synonym’, or ‘Max Dim’ can be a help. The ‘Category’, ‘Synonym’ and ‘Keywords’ columns serve to classify experiments, but can be incompletely filled in, or misleading. The Right Mouse -> Filter command is a good way to select sets of experiments; you might try filtering on ‘NOESY’, ‘TOCSY’, ‘CA’, ‘CO’, ‘H[N]’ or ‘H[C] (respectively 15N and 13C one-bond, out-and-back transfer), etc.

The following examples should get you started on the nomenclature:

HNCAHA: 4D HNCAHA prototype, starting on HN and ending on HA. The prototype
includes HNcaHA (3D), HACAnH (3D, note reversed direction), HncaHA (2D) etc.

H[N[CA[HA]]]: 4D HNCAHA prototype with out-and-back magnetisation transfer.

H[N]_H.NOESY: 3D HSQC-NOESY. Prototype includes NOESY-HSQC (H_H[N])

H{CA|Cca}NH: 4D HCBCANNH

C[h(0)]: 1D carbon, selecting quaternary carbons only.

Viewing experiment prototypes

You need to look at all the tabs to understand the experiment in detail. The Atom & Measurement tab shows which atoms are on the magnetisation transfer pathway, and which shifts etc. are being observed; the Exp Graphs tab show the magnetisation transfers and the flow of magnetisation in the experiment; and the RefExperiments tab shows the individual reference experiments and what is on the axes.

Editing experiment prototypes

Editing existing experiment prototypes is discouraged, as these are reference information and should be edited only centrally. For this reason existing prototypes are normally not editable (see below for instructions). Adding new prototypes and new RefExperiments is more likely to be useful. Ultimately it is the responsibility of anyone adding reference information to understand what he is doing, so the explanation here is focused on the simplest way to proceed.

You must always 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 simple to change atom names, parameters etc., and to remove atom sites. If this will do you, select your template experiment and press [Create Copy]. Then edit the copy, starting with the columns Name, Category, Synonym, and Keywords in the Prototypes tab, and continuing on the other tabs. The numerical columns in the ExpPrototypes table can be left alone, as the values will adjust to changes in the other tabs. Remember to rename and remove or add RefExperiments to fit.

If you need more complex operations, you are better off creating a new prototype. It is still helpful to use an existing one as inspiration.

Start on the Prototypes tab and click [Create New]. Then set the Name, Category, Synonym, and Keywords, ignoring the rest of the columns on this tab. Try to make sure you have got the nomenclature right, preferably using another prototype as a template, and that the name does not duplicate that of an existing prototype.

Now go to the Atoms & Measurements tab, and add Atom Sites and Exp Measurements. For clarity go through the Atom Sites in the order of the magnetisation flow of the experiment. Select the atom type in the pulldown menu besides the [Create new type] button and press the button to create the atom site. If you are measuring the shift (or another parameter) of this atom site, press the [Create New] button under the Exp Measurements table while the newly created atom site is still selected. This approach will minimise the number of mouse clicks. Finally edit the table contents if needed.

Now go to the Exp Graphs tab. Create a new Exp Graph in the top left table - you only need more than one if you have several distinct magnetisation transfer flows in your experiment (essentially if you have curly braces in the systematic name). Now add as many magnetisation transfer steps as you need by clicking [Create New] under the bottom table, and edit the fields in the table to get the contents right. Finally add as many ExpSteps as you need, and edit the contents. Note that this table must follow the magnetisation step by step - an HSQC experiment would have steps, in order, ‘1 Shift(H); 2 Shift (N); 1 Shift (H)’.

Finally go to the Ref Experiments tab and add the Ref Experiments. It is easiest if you start by making the RefExperiment with the highest dimensionality. There should always be a RefExperiment with the maximum dimensionality of the prototype, and with the same name as the prototype. Now add a [New ExpRefDim] in the bottom table for every dimension in your RefExperiment, and edit the bottom table. For clarity you should add the dimensions in the 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’.

Now start creating the other RefExperiments. It is good practice to have a RefExperiment 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 RefExperiment 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 RefExperiment with lower dimensionality, provided the highest-dimensionality RefExperiment was already 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 RefExperiment. 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 RefExperiment, and use them to create lower dimensionality reversed RefExperiments like you already did for the non-reversed case. Finally add any information you may have for the Synonym or Systematic Name columns of individual RefExperiments.

For many high-dimensionality experiments it will be useful to add a 2D Projection RefExperiment (and possibly a reversed version as well). For this, create a new RefExperiment (not a copy) in the top table, and give it a name of the form H[N[CO[CA]]].2D.{N;CO;CA} (for H[N[CO[CA]]]). Now go into the bottom table and add two RefExpDim, corresponding to the acquisition dimension (here H) and another dimension. At this point select the non-acquisition dimension in the bottom table, and click [Add RefExpDimRef] once for each dimension in the full prototype that is not already in the table. Finally edit the tables as desired.

NOTE: Experiment Prototypes and RefExperiments 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) this is how to make things editable: 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. If you wanted to edit the H[n[CA]] RefExperiment, for instance (hint: you do not!), you would type something like: nmrExpPrototype = top.project.findFirstNmrExpPrototype(serial=20) nmrExpPrototype.isEditable = True refExperiment = nmrExpPrototype.findFirstRefExperiment(name=’H[n[CA]]’) refExperiment.isEditable = True

References

A nomenclature and data model to describe NMR experiments. Fogh RH, Vranken WF, Boucher W, Stevens TJ, Laue ED. J Biomol NMR. 2006 Nov;36(3):147-55 (link)

Main Panel

pulldown Selected Prototype: Select the experiment prototype to operate on

Prototypes

A table of all NMR experiment prototypes

Table 1
# The serial number of the experiment prototype
Name CCPN systematic name for the experiment prototype. Reflects the magnetisation transfer network (Editable)
Atom Sites Number of atom sites in the magnetisation transfer flow(s)
Graphs Number of distinct magnetisation transfer flows
Ref Expts Number of associated reference experiments
Max Dim Maximum reference experiment dimension
Category Experiment prototype category. Classification of experiment purpose. (Editable)
Synonym Human-understandable experiment prototype synonym (Editable)
Keywords List of keywords, for search and filtering (Editable)
Details A user-editable textual comment for the experiment prototype (Editable)
isEditable? Can experiment prototype be modified? True for newly created experiments

button Create New: Make a new blank experiment prototype. Information is added subsequently

button Create Copy: Make a new experiment prototype that is a copy of the currently selected one

button Freeze: Set selected experiment prototype to be no longer modifiable

button Delete: Delete the selected experiment prototype

Atom & Measurements

Atoms and NMR measurements used within selected NMR experiment prototypes

Atom Sites

Table of atom sites

Table 2
# The serial number of the atom site
Isotope The isotope of the atom site (Editable)
Name The name of the atom site (Editable)
Min Shift The minimum allowed chemical shift of the atom site (Editable)
Max Shift The maximum allowed chemical shift of the atom site (Editable)
Min Number The minimum number of atoms in the site (Editable)
Max Number The maximum number of atoms in the site (Editable)
Number Step The number step - E.g. “a non-zero, even number” would have number_step=2, min_number=2 (Editable)

button Create New - Type: Create new atom site of the selected type

pulldown Create New - Type entry: Select atom site type to create

button Delete: Delete atom site

Exp Measurements

Table of Experimental NMR measurements recorded in experiment.

Table 3
# The serial number of the experimental measurement
Type Type of NMR measurement (Editable)
Atom Sites Atom site(s) that the measurement relates to (Editable)
Atom Site Weights Relative weights for multiple atom sites. Only for special types, like multiple quantum coherence. (Editable)

button Create New: Create new experimental measurement, using the currently selected atom site

button Delete: Delete selected experimental measurement

Exp Graphs

Graph of magnetisation transfer types, and magnetisation flow, for selected experiment prototype

ExpGraphs

Table of magnetisation flow graphs

Table 4
# The serial number of the magnetisation flow graph
PeakSign The relative sign of peaks arising from the graph (Editable)

button Create New: Create new magnetisation flow graph

button Delete: Delete selected magnetisation flow graph

ExpSteps

Table of magnetisation flow steps for selected graph.

Table 5
# Serial number of the magnetisation flow step (corresponds to creation order)
StepNumber Position of step in magnetisation flow (corresponds to flow order) (Editable)
Measurement Experimental measurement that carries the magnetisation during the step (Editable)

button Create New: Create new magnetisation flow step for selected graph. By default created with next unused experimental measurement

button Re-number: Re-number steps consecutively starting from one

button Delete: Delete selected magnetisation flow step

ExpTransfers

Table of magnetisation transfer connections between atom sites for selected graph

Table 6
# Serial number of the magnetisation transfer connection
transfer Type Type of magnetisation transfer (Editable)
AtomSite1 First atom site involved in magnetisation transfer (Editable)
AtomSite2 Second atom site involved in magnetisation transfer (Editable)
transfer ToSelf Does the transfer allow magnetisation to remain on the starting site? (Editable)

button Create New: Create new magnetisation transfer connection for selected graph

button Delete: Delete selected magnetisation transfer connection

Ref Experiments

Reference experiments belonging to selected experiment prototype with description of the experiment axes.

pulldown NamingSystem: Naming system for reference experiment systematic name

RefExperiments

Table of reference experiments included in experiment prototype

Table 7
# The serial number of the reference experiment
Name CCPN systematic name for the reference experiment. Conforms to the Experiment Prototype name. (Editable)
numDims Number of dimensions of reference experiment (Editable)
isReversed Is magnetisation transfer flow reversed relative to the experiment prototype specification? (Editable)
Synonym Human-understandable reference experiment synonym (Editable)
Systematic Name Reference experiment systematic name in selected namnig system (Editable)
isEditable Can reference experiment be modified? True for newly created experiments

button Create New: Make a new blank reference experiment . Information is added subsequently

button Create Copy: Make a new reference experiment that is a copy of the currently selected one

button Freeze: Set selected reference experiment to be no longer modifiable

button Delete: Delete the selected reference experiment

RefExpDimRefs

Table of Reference experiment dimensions and dimension referencings

Table 8
Dim Dimension number for reference experiment dimension
# Serial number for dimension referencing
expMeasurement Experimental measurement associated with dimension referencing (Editable)
valid scaling factors Scaling factors allowed when converting from observed frequencies to measurement values (Editable)
grouping number Number that classifies dimension referencings from a dimension into consistent groups. E.g.: Group 1: 13C shift and J(HC); group 2: 15N shift and J(HN) (Editable)
Coupled Isotopes Isotopes to which couplings are active and observable. Alternative to specifying couplings as experimental measurements (Editable)
Constant Time Acquisition mode: Constant, variable or mixed time. (Editable)
expSteps Experiment steps used for measuring the measurement (in cases where it matters) (Editable)

button New RefExpDim: Add new reference experiment dimension

button New RefExpDimRef: Add new dimension referencing to the same dimension as the referencing currently selected

button Delete RefExpDim: Delete selected reference experiment dimension and all dimension referencings

button Delete RefExpDimRef: Delete selected dimension referencing

button Purge RefExpDims: Delete reference experiment dimensions that have no dimension referencings. Used for removing orphan dimensions after deletions elsewhere