Hi,
Is there a way to directly change the Z-plane of one or multiple 3D spectra (HNCA and HNCO) by clicking on a peak or just the HSQC?
I usually use this function in CARA to identify the correct 3D peak in crowded regions.
Thank you.
Hi,
At the moment you can navigate to a single other SpectrumDisplay/Strip in the following ways:
- select a peak in the HSQC, right-click / Navigate to .... (select strip)
- open a PeakList module. Double-clicking on a peak will navigate to that peak.
- open an NmrChain module with a list of all the NmrAtoms. Double-clicking on an NmrAtom will navigate to that position in the currently selected Strip (the one with highlighted axes).
Navigating to the same position in multiple SpectrumDisplays is possible in the following ways:
- open the Pick&Assign module (PA). Double-clicking on an NmrAtom will (by default) take to you to that position in all Displays (though you can specify a subset in the Settings, if you prefer). If one of the Displays has strips, then they will be replaced by a single strip - unless one of the strips is the active one (axes and Strip ID highlighted in blue/green) in which case it will navigate to that strip and the others stay as they were.
- open the Sequence Graph module (SG). As above, double-clicking on an NmrAtom will (by default) take to you to that position in all Displays (though you can specify a subset in the Settings, if you prefer). If one of the Displays has strips, then they will always be replaced by a single strip.
Interestingly, I`ve never before done quite such a systematic review of our Navigation options and it strikes me there are possibly some inconsistencies here and certainly room for improvement. We do also have ideas for new/improved navigation options, including some kind of drag&drop navigation as an alternative to the right-hand mouse menu (particularly useful when you have lots of strips) and improved navigation from tables. We`re also hoping to enable `axis synching`, so axes from different Displays can be `synched` and move together. None of us on the CCPN team are familiar with CARA, so if that has options that you would find helpful, then do let us know. What you describe will also become easier once we have implemented separators/tiling - which basically enables strips which share the same Z-plane. You can then have your HNCA and HNCO in the same Spectrum Display at the same NH position and view the CA and CO regions along the y-axis without all the space in the middle.
Best wishes,
Vicky
Hi Vicky,
thanks for your fast and extensive response.
Yes an axis synching option would be very nice.
You already have a synched crosshair in the different spectra.
It would be cool to have an option in the spectrum display to sync the z-plant to the HSQC position by clicking.
For me this is very helpful (in CARA) to pick 3D peaks in crowded regions of a spectra.
If 2 or 3 peaks are close together with a similar proton frequency, I usually klick around to the edges of the peaks and compare the relative intensities of the 3D peaks. With this it can be easy to pick the correct 3D peak.
If I try to do something similar in CCPN, I would have to create manually additional `peaks` at the borders of the peaks, select them, make a strip plot and then carefully compare everything.
I would be very happy if such a sync function or navigation tool would be implemented, because picking 3D peaks in crowded regions can be very tiresome.
Thanks.
Hi,
some other thoughts on picking 3D peaks:
- if you do Shift + Ctrl/Cmd + left-drag, then the program will find the maximum for you. If this isn`t in the current plane, nothing will be picked. Moving planes may help, or by showing e.g. 3 planes (signified by the box next to the z-plane position), you are more likely to be able have the correct plane showing and be able to pick the peak.
- If you have peaks that are overlapped in 3D, it can be helpful to view the spectrum another way on. YZ will open a new display with the z and y axes swapped (XY and XZ will swap the x/y and x/z planes).
- If I have picked some overlapped peaks in an HSQC (remember you can do a group fit of them with select peaks / right-click / Refit Peak Group (or RG)), then I might put a mark through one, place the mouse on it, right-click and then navigate to the 3D and then place the peak at the marked position at that z-position. Then do the same for the other peak.
Hope these things might help you in the mean time.
Best wishes,
Vicky