In the mean time CCPNmr Analysis is probably the best NMR assignment software available and I would strongly recommend using it. For details on how to download and install it, please see the CCPN website.
Currently there is no detailed manual for CCPNmr Analysis and while the Tutorial provided on the CCPN website makes sense to anyone already familiar with protein NMR assignment, others have found it rather cryptic. A wiki-style manual is currently being put together, but is still slightly patchy. In the mean time, here is a description of the basic functionalities required for protein NMR assignment.

There are a few differences between Analysis 2.0 and 2.1, so there may be some inconsistencies with menu names etc. - but nothing drastic. I will try and update things soon.

When starting a new project begin with creating it by going to the Project pull-down menu, selecting New and giving the project a name. Analysis will create a directory called ProjectName in which it stores all the files related to the project.

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So as to be able to assign atom names to your resonances, you need to tell Analysis what molecules you are investigating. Do this by selecting Molecule Setup in the Molecules menu. You can add a protein, DNA or RNA sequence to Analysis and it will automatically generate the full molecule for you. It will also create a so-called Molecular System. Your Molecular System should contain all relevant molecules in your NMR sample. If you are just looking at a single protein then this is the only molecule that needs to be included in the Molecular System. But perhaps at a later stage you will also investigate your protein in complex with a another protein or a ligand. You will then need a second Molecular System for the complex since this will have different chemical shifts, a different structure and could require some new assignment work. Unusual amino acids and other molecules can also be added to your molecular system. Go to the Small Compounds tab in the Molecule Setup pop-up to do this or contact the CCPN team for help with how to include other molecules into your project.

To add your protein (or DNA/RNA) click on the Add Sequence tab and type or copy/paste your sequence into the box (making sure that the correct type of polymer and 1/3-letter code is selected above). You can also read the sequence in from a file using the Read File button at the bottom of the pop-up. Make use of the other options at the top of the pop-up if you need to: select the Cyclic box if your protein is cyclic. If it does not start with residue number 1, then simply enter the correct residue number for the first amino acid in your sequence into the Start Number box. Or if you are adding a second squence to a Molecule or Molecular System, then select the relevant Destination Molecule or Destination Mol System from the drop-down menus. Now click Add Sequence! at the bottom of the pop-up.

You will be asked for a New Molecule Name - it is usually helpful to choose something meaningful such as the name of the protein. Then you will be asked for the Molecular System Code - MS1 will do, but choose something else if you like. Finally you need to a specify a Chain Code - A is usually a good choice for your first molecule. For proteins you will be asked whether the Phe/Tyr Hd1/2 and He1/2 atoms are equivalent due to rotation or not. In the vast majority of cases these aromatic rings have sufficient space to be able to rotate and the Hd1/2 and He1/2 atoms will thus end up with identical chemical shifts. There are some molecules where rotation is hindered. Unless you know this to be the case for your molecule, simply click Yes.

Note that the other tabs in the Molecule Setup pop-up now contain various bits of information about the molecule you have just entered.

If your sample contains other NMR observable molecules, add these to your Molecular System, too.

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Go to the Experiment pull-down menu and choose Open Spectra. Make sure you select the correct data format at the top of the box - a large number are possible (Azara, Bruker, Felix, NMRPipe, NMRView, ucsf). Change the Experiment Name if you wish (you can always change it again at a later stage, if you want). In general, you should use a new experiment name for each spectrum you read into Analysis. It is in fact possible to read several spectra into one experiment, but this should only be done if the spectra are derived from the same data but processed differently. Change the spectrum name if desired. By default Analysis will read your spectrum into the first possible window. If you have a large number of windows or spectra you may want to change this to All or None instead (though the All option can slow you down if you have a lot of windows). In certain cases you may be using several shift lists - in that case make sure you have the correct one selected (but again this can also be changed at a later stage).

You will now see the Verify Spectra pop-up. The Verify Referencing tab shows you the referencing information. It can be worth checking that this looks reasonable and that the data was referenced correctly when processing it. When reading in Bruker data, for instance, the isotopes may not be defined correctly. Change things if necessary (though this can be done at a later stage, too). The Verify File Details gives you information on the matrix size of you spectrum - generally these are fine. Simply click OK at the top of the pop-up when you are done.

You will now be faced with the Specify Experimt Types tab of the Edit Experiments pop-up. Analysis likes to know what type of experiment each spectrum is. It is then able to do intelligent things such as automatically know that certain dimensions must belong to the same amino-acid etc. You can narrow down the experiment types on offer by selecting the Category (through-bond, through-space etc.). Then select the name either using the common names under Type Synonym or the CCPN-defined naming system under Full Type. Once you get your head round it, I find the latter easier than the former, as the common names are sometimes different to what I would use. The CCPN naming system essentially puts those atoms which are observed in capitals and those which are used for magnetisation transfer steps in the experiment in lower case. I think the transfers are generally via J-couplings except where stated otherwise (e.g NOESY, TOCSY). Click on Close - All Done at the bottom of the pop-up when you have finished selecting your experimt type.

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Each window within Analysis has a defined dimensionality (i.e. it is either 2D, 3D, 4D etc.) and the isotopes for each axis are fixed. So you might have windows with (x,y,z)=(¹H,¹⁵N) or (¹H, ¹⁵N, ¹³C) or (¹H, ¹³C, ¹⁵N) or (¹H, ¹H, ¹⁵N) etc. When you open your first spectrum, Analysis will create a window for it to be shown in. However, in some cases the window may not be the one you want: for instance an HNCO is usually opened in a (¹H,¹⁵N,¹³C) window, but personally I prefer to look at it in a (¹H,¹³C,¹⁵N) type of window. If you open further spectra and windows already exist with the correct number and types of axes, then no new window will be created - instead the spectrum is shown in those windows which are already present. When no window is present in which the spectrum will fit, a new one is created.

You can create your own windows by going to the Windows pull-down menu and selecting New Window. Simply select what axes you would like and what isotopes they should be associated with. In the lower panel Analysis will show you if there are spectra which will fit into this window. If this is the case you have the option of selecting which (if any) spectra should be shown in this window (this is particularly useful when you have lots of spectra, as the program can get very slow if it tries to draw 20 spectra on top of one another in the new window).

If you want to duplicate a window, simply go to the Edit Windows option in the Windows pull-down menu. Select the window you want to duplicate and click Clone.

The Edit Windows pop-up has a number of useful features:
Aspect Ratio: this will change the relative scaling of the x and y axes - change this to make your peaks look more round or elongated.
If you have spectra with two axes belonging to the same isotope (e.g. (¹H,¹H)), then by default these have different Panel Types (e.g. H1 and H2). If you set them both to be H1, then your mouse will become symmetric across the diagonal and show two crossing-points rather than just one. This can be very useful for spectra such as 2D H-H NOESYs or solid-state carbon-carbon correlation spectra.
You can also select to see a 1D trace of the spectrum as you move across it with the mouse - displayed either on the mouse (X/Y cross-hair trace) or along the side of the spectrum (Side Trace). You can switch these settings on and off in the Edit Windows pop-up, but in practice it is easier to do this via the mouse under the Right Click / Window option. To change the scale of the 1D traces use the Home and End keys.

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There are a number of ways in which you can change the appearance of your spectra. A number of things can be changed under Edit Spectra in the Experiments menu. The Display Options tab allows you to change the colour of your positive and negative contours. You can also order you spectra which will define the order in which they are drawn on top of each other and the order in which their buttons appear in the spectrum toolbar. You can also give your spectrum a keyboard short-cut. The Referencing tab allows to change the spectrum referencing at any point. In the Tolerances tab you can change the ppm tolerances within which Analysis looks for assignment options. This is particularly useful for solid-state NMR, since larger tolerances are often needed here.

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Analysis has some extremely nice ways of moving around your spectra using the mouse and keyboard.

Zoom:
(a) roll your mouse wheel
(b) press mouse wheel/middle button + Shift, then move the mouse

Moving around the spectrum:
(a) press mouse wheel/middle button and move the mouse
(b) use the scroll bars

Moving through z-planes:
(a) roll the mouse wheel while holding down Ctrl
(b) use the scroll bar

To go from a place in one spectrum to an identical place in another:
Right click the mouse and go to Navigate, then select the relevant window (and whether you would like identical axes to be swapped or not)

To increase/decrease the z-plane thickness:
make the z-plane scroll bar thicker or thinner by pressing the middle mouse button on the edge of it and dragging.

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Analysis can draw marks and rulers. The difference is that rulers are only drawn in one dimension (horizontal or vertical) where as marks are drawn in all dimensions. When you draw a mark or ruler in one window, it is automatically also drawn in all other windows. This is a very useful way of checking whether peaks are really at the same height or not. To draw a ruler press h or v for horizontal and vertical rulers, respectively, and it will be drawn at the current mouse position. To draw a mark, press m. n will remove all marks and rulers. You can also draw marks and rulers using the Marker menu in your Right Click mouse menu. This also allows you to remove only marks or only rulers rather than all at the same time. By default only one mark and ruler can be drawn at any one time (i.e. if you draw a second, the first goes away). To increase the number you can draw, go to the Windows menu and select Marks and Rulers. Here you can also select the colour of your marks and rulers. Marks have the added feature that if you draw them near to a peak, they will automatically position themselves on the peak and be black. Otherwise they will go at the precise mouse position and be the colour selected in the Marks and Rulers pop-up.

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You can pick peaks by positioning the mouse where you would like to have one and then Right Click the mouse and select Add new peak from the Peak menu. Alternatively, a better way is to drag the mouse over a region while holding down Shift and Crtl - this will place peaks at any maximum in that region. It is worth being aware of the Peak Finding pop-up in the Peaks menu. Here you can define a number of parameters which relate to peak picking. By default only positive peaks are picked, but here you can change this to negative only or positive and negative. Other parameters (which I hardly ever change, but you might find useful) include whether peaks are picked on, above or below the contour level and the method by which the volume of a peak is calculated. In the Diagonal Exclusions tab you can set Analysis to exclude certain regions close to a diagonal from being peak picked. Using the Region Peak Find tab you can peak pick a restricted part of your spectrum by specifically including or excluding certain regions from the peak picking procedure

The volume of a peak is calculated at the time when it is picked which means that you do not need to perform an additional peak integration step if you want to get a peak volumes.

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Analysis is based around the concept of a Resonance - it makes sense, but is difficult to explain. But I will try. Each resonance is associated with one particular atom in your molecule. In theory you might think that it is associated with the particular chemical shift of that atom, but the reason for having the concept of a resonance, is that the chemical shift itself is dependent on many outside influences, such as temperature, pH, salt, ligand etc. This means that any one atom is not associated with any one particular chemical shift. Thus the resonance is there to hold it all together. The reason why you can't simply use the atom as your central object is that to start with you obviously don't know which peak corresponds to which atom.

When you pick a peak in Analysis the first thing you have to do to it, is create a new resonance for each dimension. At a later stage you may then add further attributes such as the atom type (Cα or Cβ), or the full assignment, i.e. exactly which atom in the molecule it corresponds to (Asp10Cα or Trp54N). Resonances are numbered from one upwards and are always shown in square brackets in the peak labels and can be looked at and manipulated using the Resonance Table which can be called up from the Resonance pull-down menu. The Resonance Table is also useful for navigation purposes, as you can mark selected resonances and go to their position within a specified window.

A spin system basically contains all resonances which belong to one amino acid in a protein (or one nucleotide in DNA/RNA or one sugar ring in a carbohydrate). When two resonances are known to be in the same spin system they can be added to a new spin system. Spin systems are initially numbered one upwards and their numbers are shown in curly brackets in the peak labels. Spin systems can be manipulated in the Spin Systems pop-up which is accessed via the Resonance menu. It is possible to associate a spin system with a particular amino acid type and also to merge them (e.g. if resonances originally associated with separate spin systems later turn out to belong to the same one).

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Peaks can be assigned by using the Assignment Panel in the Assignment menu. Alternatively, you can access it by holding the mouse over a peak and pressing a or doing Right Click / Assign / Assign Spectrum. The Assignment Panel can also be called directly from a Peak Table in the Peak Lists pop-up. The Assignment Panel will show a field for each dimension of the peak. On the left there is the information on isotope type and chemical shift and what assignments have been made for the peak. On the right hand side are possible assignment options. Note that more than one assignment can be made for a single peak (as it may be the result of two overlapping resonances).

Several options are available. Of particular note are the Double Tolerances and Correlated Dims options. By default each spectrum has certain tolerances for each dimension within which Analysis will look for assignment options. Sometimes it is useful to double this when doing assignments, if the peaks are slightly off in the different spectra. The tolerances can be changed for spectra by calling the Tolerances pop-up from within the Edit Spectrum pop-up.

The Correlated Dims option makes use of the fact that the experiment type is known and that for some experiments certain dimensions have to belong to the same spin system. For example for a peak in an HSQC spectrum the two dimensions (H and N) have to belong to the same spin system (residue). Thus, if Correlated Dims is selected, only those options are shown where both dimension fit to the same spin system - a useful way of reducing your assignment options quickly.

If you are doing assignments in the solid state and are using a glycerol labelling scheme, then you can select this using the Labelling Scheme drop-down menu.

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By default each spectrum has one peak list associated with it. But you can add extra (empty) ones, duplicate (clone) peak lists, read in a peak list from another programme (using the Format Converter) or create a synthetic list from data such as chemical shift lists or structural data. Only one peak list is active at any one time, so if you are working with several peak lists, then make sure the correct one is active. Under Peak Lists in the Peaks menu you can see and manage all your peak lists.

To actually look at a particular list and the peaks within it, go to the Peak Table tab in the Peak Lists pop-up. A useful feature within this pop-up is the ability to choose a window from the top right hand drop-down menu and then go to Find Peak. That window will then centre on the selected peak and be marked with a thick black mark.

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Strips are particularly useful when doing assignments. Basically it is a way of seeing several parts of a 3D spectrum next to one another at differing z-planes (see Visualising 3D Spectra for more information on strips). To manage your strips click Strips in your Spectrum Window Toolbar. + will add strips. The strips are numbered (top left hand corner) and the z-plane is displayed in the bottom left hand corner of each strip. There is a button for each strip and the active one is coloured green. - will remove the active strip and Clear will remove all strips. The Left Arrow and Right Arrow will move the active strip one place to the left or right; in this way you can change the order of your strips. Note that if you navigate from another window into a window containing strips, you will navigate to the active strip. The little button with three bars on it, specifies whether your strips will be vertical or horizontal. In general, vertical strips are used, espcially in solution NMR. However, for solid-state MAS NMR spectra it is often convenient to use horizontal strips. Simply click the little button with the bars to switch between vertical or horizontal strips.

A further feature in Analysis is that you can add so-called Separators. If you Right Click the mouse and go to Strips you will find that if you are in vertical strip mode you can Add a horizontal separator and vice versa. This allows you focus on two different parts of your your spectrum in the same window. E.g. you can look at the aliphatic and carbonyl regions of a spectrum above and below your separator and thereby remove from view the less interesting region in the middle of the spectrum. You can use a separator whether you are using strips or not.

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All tables in Analysis have some basic elements in common. Cells which can be edited by the user have a small E in the bottom left hand corner. Columns can be sorted by clicking on the column header. A small arrow then indicates the direction of sorting. Repeated clicking reverses the order. In any table it is possible to Right Click the mouse and then select Filter so as to filter for certain strings (generally or in particular columns). It is also possible to Right Click the mouse and select Export so as to export any combination of columns to a tab- or comma-separated file.

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There are numerous keyboard shortcuts. You can see what these are and also change them if you go to Macros and then Organise Macros. Here is a list of the default settings:

Spectrum Manipulations

Marks and Rulers

Pop-Ups

Peaks

Other

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