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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 Spectrum groups and the ability to save Layouts.

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 still to be implemented.

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 as many features.

Pseudo-3D spectra

It isn't currently possible to open pseudo-3D spectra in V3 as in Version 2. We are still deciding exactly how to implement this.

Reference Chemical Shifts

You can view these with RC, but the graphs are not yet as interactive as in V2 and do not show a cursor linked to the other spectrum windows. Our intention is to expand the capabilities, so that you can eventually add your own reference data. E.g. if you are working with intrinsically disordered proteins, you could import a different set of reference chemical shifts suitable to these types of proteins.

Synthetic peak lists

It is currently possible to create a synthetic peak list when importing a BMRB file (see BMRB Import), but not from a chemical shift list or pdb file (unless you try writing your own macro).

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 pdf tutorial and publication for more information.

Follow Intensity Changes

This will be implemented in a similar way to the Chemical Shift Perturbation module.

Shift Differences

Not yet implemented

Heteronuclear NOE analysis

Not yet implemented

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

Not yet implemented

Secondary Structure Chart

Not yet implemented

Quality Reports

Not yet implemented, but our intention is that amongst other things these will give you the tables/information you need to report in publications.

Structure related features

These features are grouped under the AnalysisStructure programme which is still under development. It is possible to read in pdb files and restraint data from NEF files, but otherwise few structure-related features are implemented as yet.

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. CYANA, YASARA and XPLOR-NIH, PDBStat) are also starting read and write NEF files and others (ARIA, AMBER, PSVS) will be implementing this soon.
A temporary alternative to export data to other programmes will be to use our new V2.5 (to be released in the coming weeks) to read in a NEF file and then you can use the FormatConverter from there.