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Popular V2 Features in V3

Popular V2 Features in V3

As we implement popular V2 features in V3, we are aiming not just to replicate them, but to improve and expand them as well. Of course, this takes time and not all V2 features are yet implemented in V3, but we are working on this!

We also have a page showing the V2-V3 translation of mouse/keyboard functionality.

Spectrum customisation

This has become somewhat easier. See our Customise Spectrum Display video tutorial for more information.

Spectrum organisation

This has become easier through the use of SpectrumGroups. See our Organising Spectra with SpectrumGroups video tutorial for more information.

Marks and Rulers

From V3.0.1 you can place marks with MK (mark mouse position) and PM (mark selected peak(s)) and rulers with MX, MY, MZ (at mouse position in X/Y/Z dimensions) and PX, PY, PZ (at selected peak(s) in X/Y/Z dimensions). MC clears all marks and rulers. Marks and rulers currently all have the same colour which can be selected in the Preferences dialog (Ctrl/Cmd + ,). In future, we hope to make it possible to selectively delete individual marks/rulers.

Printing

The print dialog now offers even more detailed customisation of which features to print. Additionally, files can be saved in .svg as well as .pdf format. Printing a defined region is implemented from version 3.1 onwards. See our Printing to File video tutorial for more information.

Tentative Assignments

These no longer explicitly exist in V3, because they are no longer needed in the same way. The fields containing the NmrAtom names, NmrResidue names and NmrResidue sequence numbers are in fact free text boxes. So you can enter anything you want, e.g. HB/HG or 23/45/139 or Asn/Asp might signify that you have narrowed the assignment down to just two or three options. Or 23? might signify that you are not quite sure about your assignment. Once you know what the assignment should be, you can change it any time by double-clicking on the NmrAtom/NmrResidue in the sidebar and making the change in the NmrAtom/NmrResidue Editor.

Tiles / separators in spectrum displays

Not yet implemented.

Assignment Graph

V3 has the Sequence Graph which is similar to the V2 assignment graph, but doesn't currently include quite as many options.

Pseudo-3D spectra

This is implemented from Version 3.1 onwards. See our Working with Pseudo 3Ds video tutorial for more information.

Reference Chemical Shifts

You can view these with RC or go to Molecules / Reference Chemical Shifts.

Synthetic peak lists

You can create a synthetic peak list by right-clicking on a ChemicalShiftList in the sidebar and selecting Simulate Spectrum. The number of types of spectra you can create PeakLists for is still somewhat limited. But do contact us, if there is a particular type of spectrum you would like added, as we may be able to implement it relatively quickly. It isn't possible to create synthetic PeakLists for through-space spectra yet.

Follow Shift Changes

This is implemented as our new Chemical Shift Perturbation module. This is more developed than the V2 feature. You can set the threshold interactively and look at the results on a structure in PyMol directly. It doesn't, however, currently include the automatic tracking of peaks. See our Chemical Shift Perturbation Analysis tutorial and publication for more information.

Follow Intensity Changes

This is implemented as part ouf our Relaxation Analysis Module. Have a look at our Dynamics tutorial for more information.

Shift Differences

Not yet implemented

Heteronuclear NOE analysis

This is implemented as part ouf our Relaxation Analysis Module. Have a look at our Dynamics tutorial for more information.

Analysis of 3J H-Ha Couplings

Not yet implemented

Horizontal Strips

You can switch any Spectrum Display module to show horizontal (row-style) rather than vertical (column-style) strips. Simply go to the Spectrum Display settings (gear icon) and select your preferred strip arrangement. From V3.0.1 onwards, the Z-plane scrolling can be switched to a new "in-display" setting. This saves space in horizontal/row strip mode by removing the individual Z-plane scroll bars for every strip and placing them below the strip ID instead.

Initialise Amide Side-Chains

This is has so far been implemented in a slightly more basic way compared to V2. After setting up the NmrResidues in your HSQC, select two peaks which belong to an NH2 pair and then go to Macro / Run CCPN Macros / setupNH2SideChainPair.

Secondary Structure Chart

Not yet implemented

Quality Reports

Not yet implemented, but we have a macro for this coming in Version 3.2.3 (Spring 2024).

Structure related features

These features are grouped under the AnalysisStructure programme which is still under development. Have a look at our Structure tutorial for details about this.

Isotope Labelling

At the moment we have no plans to include this in V3, as it does not appear to be used much. If you think this is important, then please do contact us to discuss this.

Format Converter

Version 3 doesn't have a format converter the way that V2 does. This is because all major NMR programme developers and deposition databases have now committed to using the new NMR Exchange format (NEF). This format will make sure that important information, e.g. on stereospecific assignments etc., is not lost (as is currently the case).
V3 can export any part of the project as NMR Exchange Format (NEF) files. Both the PDB and BMRB will accept NEF files when you deposit your data. Several structure calculation and validation programmes (e.g. ARIA, Amber, CYANA, NMRtist, PDBStat, YASARA and XPLOR-NIH) are reading and writing NEF files and others (PSVS) will be implementing this soon.
You can also use Gary Thompson's NEF pipelines to do some format conversion. Have a look at our NEF Pipelines tutorial for more details on how to use this.
Another workaround to export data to other programmes is to use V2.5.2 to read in a NEF file and then you can use the FormatConverter from there.