Functionality
Which versions of Aria and Analysis are compatible?
The current version of ARIA, 2.3, is compatible with version 2 of CcpNmr Analysis. The previous version of ARIA, 2.2, is only compatible with CcpNmr version 1 projects.
How can I export data from an Analysis project, for example a chemical shift list?
There are various options to export data from an Analysis project:
Export directly from the table data: From the table of data, e.g. the chemical shift list, click right mouse and select Export (R: Export), which will open the Export Data popup that can be used to export the data to a text file. The order of the output can be defined by sorting the columns by clicking on the column headers first.
Export via the FormatConverter in a particular existing NMR data format. Go to M: Other: FormatConverter, which will open the FormatConverter popup. From there, go to "Export", select the format you want to export to and follow the instructions provided by the program.
Is it possible to extract 1D slices from a 2D spectrum and to display them?
There are a various possibilities to extract and display 1D slices of a 2D spectrum:
You can add side traces to a window. Go to the R: Window: Add side traces and adjust R: Window: Slice size as appropriate. These 1D slices follow the cursor. Use the 'Home' and 'End' keys to scale to 1D views.
You can create a more permanent view by making a dedicated 'Value' window which is effectively a 1D slice of higher dim spectra. Go to Menu M: Window: New Window and select "value" for the Y axis and the correct isotopes for X and Z axes. - e.g. if you want to display a 1H slice of a 3D select 1H as X axis and the other nuclei as the Z axes. Moving through the Z axes will allow you to change which slice is viewed. You can navigate to this window from any point in others (that share the axes) in the usual way. - R: Navigate.
Is it possible to automate repetitive tasks?
Yes it is possible to automate repetitive tasks. In some cases, for example when multiple objects have to be manipulated in the same way, repetitive tasks can be performed at once by simply selecting all objects that need to under go the same procedure. A simple example thereof is for example selecting the complete contents of a peak list and deassigning all peaks at once.
In more complicated cases, repetitive tasks can be automated with Macros, of which an example is the "Initialise Root Resonances" macro that can be activated from M: Assignment: Initialise Root Resonances menu. Guidelines to writing macros can be found here.
Is there a way of recording commands for storage in a macro?
Unfortunately, commands currently can not be recorded for storage in a macro.
How can I transpose or change the axes in a multidimensional spectrum?
There are 2 ways of transposing spectra:
In case a spectrum contains multiple axes of the same type, e.g. 2 1H axes, the |Dim. Mapping| in the {Spectrum & Peak Lists Mappings} tab, accessible through M: Window: Windows popup can be changed by swapping the dimensions.
In all cases you can simply create a new window using M: Window: New Window, and set the axes to meet your needs.
How can I pick negative peaks?
The behaviour of the peak picking routines can be set in the Peak: Peak Finding popup (M: Peak: Peak Finding), in which you can specify which kind of peaks to pick and with which parameters.
I have recorded a spectrum with a large sweep width, but can only see part of it in the Analysis spectrum window. How can I display the full spectrum?
Analysis contains definitions for spectrum regions that are displayed in each dimension / windows axis. Spectra may be recorded with very large sweep widths, for example in order to find all peaks at their unaliased frequencies, that exceed the default region settings in Analysis for the given axis and part of the spectrum is not visible. To change this, go to the Window: Axes popup (M: Window: Axes), {Axis Types} tab, and change the |Region| parameter to match the spectrum width of your spectrum.
What are regular expressions and how do I use them when filtering tables?
In computing, regular expressions provide a concise and flexible means for identifying strings of text of interest, such as particular characters, words, or patterns of characters. Analysis uses regular expressions, for example in the Filter Options popup (R: Filter), where it can be used to select a certain subset of of a table. For example, in case you want to filter a resonance list on Hn's only you can use the regular expression
H\s|H$ for the Assign Name column in the resonance list. The | means "either"; the \s matches whitespace, and the $ means the end of the string. So the above
matches H followed by whitespace or H at the end of the string. Since Analysis is built on python, the python regular expression syntax applies. For more information please visit http://www.python.org/doc/2.5.2/lib/re-syntax.html.
How can I see unaliased signals for a certain dimension?
To see unaliased signals, you can change the minimum and maximum aliased frequencies, which are set in the Experiment: Spectra popup, tab {Referencing}, which can be accessed through M: Experiment: Spectra. In case a spectrum is aliased, extending the minimum and maximum aliased frequencies such that they span the unaliased (or real) frequencies will display the signals at their unaliased frequencies. For more about Aliasing see the Core Concepts and the HowTos.
Note that each axis type has a range of expected (shown) frequencies, which can be set in the Window: Axes popup, tab {Axis Types} using M: Window: Axes. There you can change the minimum and maximum frequency for a certain axis type. These settings limit the settings for the minimum and maximum aliased frequencies.
Why can I not assign PeakDim Xxx to Atom Yyy?
Each peak dimension is associated with a certain nucleus type or isotope, which is defined in the experiment. Each resonance also has an isotope associated with it, and to assign a peak dimension to a resonance, the isotope of the resonance has to match the isotope of the peak dimension that you want to assign.
I am assigning a resonance to a non-stereospecific atom assignment Hβb, but Analysis changes the assignment to Hβa. Why is this
The user has no choice with regard to which of the "a" or "b" labels is used for non-stereospecific assignments. Analysis sets the label for the user in the correct manner. The labels are usually allocated according to the chemical shifts; "a" is the lower ppm value and "b" the higher ppm value. If only one resonance of the pair is assigned then "a" is used, hence this may switch to "b" if the other resonance of the pair is assigned to a lower ppm value.
The only instance where the rule is different is where non-stereospecific 1H resonances are connected to heavy atom resonances, for example Valine Cγa,Hγa* or Cγb,Hγb*. Here consistency between the a/b label for the hydrogen and the bound atom are enforced. The hydrogen resonance determines the a/b label, again according to shift value, and the carbon inherits the same label, irrespective of its chemical shift value. This way we never get mixed annotations like Cγa-Hγb* for linked resonances.
Atom type (no residue) settings for a non-stereospecific resonance can be made and results in both of the stereospecific atom names being displayed without an a/b label. For example a typed resonance may be labelled Hβ2|Hβ3, which becomes Hβa or Hβb when the specific atom and residue of the resonance are known.
Why does Hδa* show up as bound to Cδb and vice versa?
The a/b consistency is governed by covalent bonds. When non-stereospecific 1H resonances are connected to heavy atom resonances, for example
Valine Cγa,Hγa* or Cγb,Hγb*, consistency between the a/b label for the hydrogen and the bound atom are enforced. The hydrogen resonance determines the a/b label, again according to shift value, and the carbon inherits the same label, irrespective of its chemical shift value. This way we never get mixed annotations like Cγa-Hγb* for linked resonances.
However, the “a/b consistency governed by covalent bonds” could be ambiguous if there are problems in the assignment that mean Analysis can't tell which is bound to which. For example incorrect links from both Hδa* and Hδb* to Cδb. The error is likely to be one of two things:
Incorrect assignments, where the user has a wrong 1H - 13C pairing on one or more peak assignments, between dimensions that represent a covalent bond (e.g. 13C HSQC).
The assignments could be notionally correct, but the experiment type settings may have the wrong dimensions labelled as covalently bound, thus the wrong peak dimensions are used to connect bound resonances. Stereospecific mismatches like Hδ2*-Cδ1 are still possible, but usually this is just an assignment mistake rather than the experiment type. The quality reports for resonances will show these kinds of errors.
Why do I see my spectra twice – why are there 'ghost peaks'?
The ‘ghost peaks’ are seen because the minimum and maximum aliased frequencies are set outside the original spectrum boundaries. The minimum and maximum aliased frequencies are usually adapted in order to unalias peaks in aliased spectra, and can be set in the Experiment: Spectra popup, tab {Referencing}, using M: Experiment: Spectra. See the Core Concepts for more about this.
How can I change my molecule/sequence without losing the work already done on it?
It is not possible to edit a sequence once assignments are present. Create instead a new molecule from the required sequence in which you then can copy the assignments to. Copy the assignments to a new molecule in the Assignment: Copy Assignments popup, tab {Between Molecule Chains}, using M: Assignment: Copy Assignments.
My sequential assignments are doing funny things – how can I get back to a clean slate?
There are several ways to clean up a project after incorrect assignments were made, for example:
To remove sequential links between residues in Analysis, open the Assignment: Protein Sequence Assignment popup using M: Assignment: Protein Sequence Assignment. In the {Spin System Table} tab, choose a residue and click the button [Clear i+1 Links] or [Clear i-1 Links] to clear the sequential links to the i+1 or i-1 residue respectively. To remove all sequential links in the project, click [Clear All Links]. The Sequential links can also be viewed in the {Seq. Links} tab of the Resonance: Spin Systems popup
To manage and inspect a spin system (or residue). Use M: Resonance: Spin Systems and go to the {Assignments} tab. Here it is possible to separately show and modify resonances [Show Resonances] and inspect peaks [Show Peaks] for each spin system. Spin systems belonging to the same residue can be merged by selecting the spin systems and clicking [Merge]. To display peaks in a spin system in strips or in cells, select a spin system, choose window and click [Display Cells] or [Display Strips], respectively. Resonances are always left in a project until they have been deleted. When a resonance no longer is bound to a peak, it has become an orphan an it can be deleted using the button [Delete Orphans], which is available in several popups that lists resonances. For example, in the Resonance: Resonances popup.
How can I download a ‘.str’ file from the BMRB and create new peak lists based on the chemical shifts?
Go to the following web page to get the BMRB file: http://www.bmrb.wisc.edu/cgi-bin/nmrbrowse.cgi. Type in an accession number, or other details and click [Send Request]. Assuming a match is found, click on the name of the entry in the “List of .. Matching ID Codes” at the bottom of the page. On the subsequent page the .str file is located at the upper “Link to Entry:”. Right click and save the link to a directory to get the file. (You may have to type in a sensible file name like bmr1234.str)
To load the data in Analysis go to M: Project: Import: NMR-STAR 2.1.1, navigate to the .str file, click on it and [OK]. You may be asked about "molecular system" which is a cryptic way of "saying which sequence does the data relate to?". Select the appropriate code (usually "MS1" or the name of your molecule) and hit [OK]. In some cases are the sequence automatically added to a new or existing molecular system without asking.
Assuming your data has shift assignments go to M: Other: FormatConverter. Enter Process: Run linkResonances. Click [Yes] for the question about doing things automatically with default settings. Select the molecular system if the Select molecular system popup is raised. If you then get a Link chains popup then the idea is that you change the pulldown menu(s) in the middle so that the chains in the assignment (e.g. "A", "B" etc ) get connected to the sequence that was in the BMRB file, so normally you change from "Do not link" to select "Link to code 'mySeqName' ", where 'mySeqName' is the name of the sequence in the BMRB file.
Assuming the import works you should have a new shift list named after the file in the project. To make peak lists using the imported shift list go to the {Synthetic Lists} tab in the Peak: Peak Lists popup using M: Peak: Peak Lists: Synthetic Lists. In the top panel set the “Spectrum” and the “Shift List:” to be the new one, then hit the big [Predict from Shifts] button.
If the peaks are not in exactly the right place then you have two options:
You can move the imported peaks. First make sure the new peak list is set to active under |Active| in the {Peak Lists} tab in the Peak: Peak Lists popup (M: Peak: Peak Lists). Now, select a peak in the spectrum, draw the mouse cursor to the new position and click ‘p’, or snap it automatically (can do many peaks at once here) to the extremum with ‘P’. More about this is found here. If the whole peak list has an off-set it’s possible to correct this in the {Peak List} tab in the Peak: Peak List popup. To do this, select the peak list and click [Shift Whole Peak List] after which you can set the differences in ppm.
Copy the imported assignments to a separate peak list that has been picked at the correct locations. This is done in the {Between Peak Lists} tab in the Assignment: Copy Assignments popup, accessible through M: Assignment: Copy Assignments. Select the new synthetic list with assignments as "Source" and the existing list as "Target". If the ppm distance threshold is good then you may like to use the [Assign All Singly Matched] button. Otherwise, click on individual source peaks and then the desired target below and click [Assign Selected Target]. More about this is found here.
How can I add a small compound to my project?
To add a small compound to your project, navigate to the {Small Compounds} tab in the Molecule: Molecules popup, using M: Molecule: Molecules. Set “Destination Molecule:” and “Mol Type:”. Select the compound and click [Add Compound]. Note that the destination molecule has to be “unlocked”, or in other words, unassigned to a molecular system. More about this is explained here.
The chemical component (ChemComp) is in many cases not available locally. This will in such a case raise the Query popup, in which it is possible to download the chemical component to the local database. Clicking [OK] in the Query popup will often raise the Warning popup, in which it is said that no atom coordinates are available for the ChemComp. This is normal, many ChemComps do not have coordinates, and the only difference it makes is that you cannot view it in the molecular viewer.