Commands/tools for backbone/sidechain/NOE assignments using HNCA,4D-NOESY and CCH-TOCSY:

Step 0 : open all necessary spectra.

Step 1 : create a new window and add the dataset of 15N-edited 4D NOESY as a reference NOE spectrum (Windows->Add).

Step 2 : set the parameters for "4D NOE Assignment" (Assign->SEE). Please refer to menu "4D Assign" for more details.

Step 3 : set the parameters for "HNCA-4DNOE Assignment"(Assign->SEE). Select or keyin spectra names for HNCA/HNCOCA/CCH-Tocsy/reference NOESY.

Notes:
1. If the peaklist name of HSQC (or HNCA) is different from its spectrum name, setting of HSQC(HNCA) peaklist name is also required.
2. If you save the setting into a file with a default name, "hnoe.input", in current working folder, all the parameters will be automatically read when you open this window next time.
3. When you start a new NMRView and have two setting files with default names (4d.input & hnoe.input) in the same working folder:
Use command, "autohnoe", to auto-load the saved state and all the saved setting after opening your STR file.
Alternatively, click main menu "File" -> "AutoLoad All"

After setting, the following commands and hotkeys can be applied to start chemical shift (CS) and NOE assignments.

hncamp (or hm) ?H_Tolerance? ?N_Tolerance? ?C_Tolerance? ?HSQC_PeakNumber?
Sequential assignment of HSQC peak based on Ca CS of HNCA
For example:
hncamp 0.02 0.2 0.1 99
hm 0.02 0.2 0.1 99
=>In the popup window, click the button of each HSQC peak number to show the corresponding spectra (equal to middle-doubleclick a HSQC peak).

ss1 ?HSQC_PeakNumber?
draw the 15N-edited NOE spectrum based on 15N/HN CS of a HSQC peak (peak number).
For example:
ss1 12

ss2 ?HSQC_PeakNumber?
draw the reference NOE spectrum based on 15N/HN CS of 15N/HN CS of a HSQC peak (peak number).
For example:
ss2 12

xx1 ?Residue_Number?
draw the 15N-edited NOE spectrum based on 15N/HN CS of a residue (residue number).
For example:
xx1 12

xx2 ?Residue_Number?
draw the reference NOE spectrum based on 15N/HN CS of 15N/HN CS of a residue (residue number).
For example:
xx2 12

Hotkeys & Click

For HSQC only:

a: draw the reference NOE spectrum based on 15N/HN CS of a HSQC peak. This hotkey is equal to the command "ss2 ?HSQC_PeakNumber?"

m: this hotkey is the same as the command "hncamp" using default tolerances (0.02 0.2 0.1).
To change the tolerances, use the following commands:
set Ctol ?CA_tolerance?
set Ntol ?N_tolerance?
set Htol ?HN_tolerance?
For example:
set Ctol 0.2

doubleclick:
1) Left: draw 4D NOESY spectrum based on 15N/HN CS of a HSQC peak.
2) Middle: draw 4D NOESY, 3D HNCA and 3D HNCOCA spectra simultaneously.

For 4D NOESY only:

z: convert 13C/CH CS of an NOE peak into 15N/HN CS and display the corresponding peak in HSQC spectrum.

doubleclick:
1) Left: popup a window for NOE assignment.
2) Middle: draw 3D CCH Tocsy spectrum based on 13C/CH CS of an NOE peak.

Optional command:

spectrasso ?1stNumber? ?2ndNumber?
Associate several 2D/3D/4D spectra to a base spectrum(2D/3D/4D). Totally two base spectra can be bound and their associated spectra's numbers are defined by 1sNumber and 2ndNumber, respectively.
For example:
spectrasso 3 1
In the popup window, keyin or select base spectra & their associated spectra and click 'OK'. Then, doubleclick (middle button) a peak in one base spectrum and its corresponding slices will be displayed in associated spectra. If you want to associate to only one base, set 2ndNumber to 0.

Important Notes:Be careful to any folding peaks in BaseSpectra. If the SW of the dimmension with folding peaks is different from the corresponding one in associated spectra, they will not be displayed correctly!!!