Delta Release Notes v504 E[1]
Short Description
Delta Release Notes...
Description
Delta NMR Software Release Notes V5.0.4
JEOL RESONANCE, Inc. July 2013
Delta NMR Software Release Notes V5.0.4
CONTENTS 1 2 3
Copyright notice............................................................................... 1 Supported instruments .................................................................... 1 Delta Installation Instructions ......................................................... 2
4
Known Issues ................................................................................... 3
5
Changes in Delta V5.0.4................................................................. 14
4.1
Solutions when Delta freezes........................................................................3 4.1.1 Step a (Restart the Delta program on the workstation) .............................. 3 4.1.2 Step b (Restart the Control program on the spectrometer) ........................ 7 4.2 Memory leak and handle leak .......................................................................9 4.3 Gradient shim is not run .............................................................................10 4.4 Resolution is bad when gradient shim is measured ....................................12 4.5 How to update the [Parameter Bar] at the Spectrometer Control window .......................................................................................................13 4.6 Measurements are automatically run upon restarting the spectrometer side ........................................................................................14 5.1 5.2 5.3
Changes summary.......................................................................................14 Details of changes .......................................................................................14 Additional pulse sequences .........................................................................17 5.3.1 single_pulse_wet_180_slp....................................................................... 17 5.3.2 std_tocsy_pfg_phase_pn.......................................................................... 19 5.3.3 std_tocsy_wgh_pfg_phase_pn ................................................................. 21 5.3.4 waterlogsy ............................................................................................... 23 5.3.5 waterlogsy_wf ......................................................................................... 25
Delta NMR Software Release Notes V5.0.4
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Copyright notice ●
Copyright © Copyright JEOL RESONANCE, Inc. 2012, All rights reserved.
JEOL RESONANCE, Inc. 1-2 Musashino 3-Chome Akishima Tokyo 196-8558 Japan http://www.j-resonance.com ●
Trademarks • • • •
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®
®
Acrobat , PDF are trademarks of Adobe Systems Incorporated. ® OpenGL is a trademark of SGI Corporation. ® Mac OS X is a trademark of Apple Computer, Inc. ® ® ® Windows , Windows XP , Windows Vista are trademarks of Microsoft Corporation
Supported instruments ■ Minimum Recommended Configurations and Supported Workstations
• Windows XP SP3/VISTA/7 for 32bit Intel compatible computers * • Mac OS X (10.4.11 , 10.5.x, 10.6.x, and 10.7.x) for 32bit Intel based Apple computers * - Preview under OS X 10.4.x is not able to open the Delta PDF manuals.
All systems • 2GB RAM or better ® • 1.5GHz Intel Processor • OpenGL Accelerated 3D Graphics Card • CD-ROM or Media Reader • Ethernet • 1280 × 800 pixels 16bit Color Display or lager ■ Supported JEOL RESONANCE Spectrometers
Spectrometer Types ECAII, ECXII, ECA, ECX, ECS Spectrometer Control Systems Rev B (GE VME 7751) Rev C (1U Server with USB interface) Please contact your local JEOL RESONANCE representative for information regarding upgrading your spectrometer to Delta v5.0.3. The Delta v5.0.3 software can be used for data processing from any earlier version of Delta software.
Delta NMR Software Release Notes V5.0.4
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3
Delta Installation Instructions ■ Installation from Web Kit on Windows/Mac OS X
1. Login to an Administrator account. 2. Download Delta from the NMR Support web site software page at 3. 4. 5.
6.
http://nmrsupport.jeol.com Navigate with Windows Explorer or OS X Finder to the location you downloaded Delta Web kit to. Double click on the zip / dmg file to open it. Double-click on the Delta installer program, and follow the instructions. It should not be necessary to extract the exe file from the zip to run it. Delta will need a license key after installation. Use the [Options] → [License Key] menu to set the license key. If you already have a Delta License Key, there is no need to apply for a new one. The current Delta License Key will continue to work. Restart Delta after installing the license key, Delta is now ready for use.
■ Installation from CD-ROM on Windows
1. Login to an Administrator account. 2. Insert the Delta Software CD-ROM into the computer or mount the media 3. 4. 5. 6. 7.
device. Explore to the CD-ROM from My Computer and then open the Delta¥Windows folder. Double-click on the Delta install program, and follow the instructions presented. Once Delta is installed and if so desired, double-click on the Manuals install program and follow the instructions presented. Eject the CD-ROM once the installation is complete. Delta will need a license key after installation. Use the [Options] → [License Key] menu to set the license key. If you already have a Delta License Key, there is no need to apply for a new one.
The current Delta License Key will continue to work.
8. Restart Delta after installing the license key and it is now ready for use. ■ Installation from CD-ROM, Mac OS X
1. Insert the Delta Software CD-ROM into the computer or mount the media 2. 3. 4. 5.
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device. Use Finder to navigate to the CD-ROM and then open the Delta/Mac_OS_X folder. Double-click on the Delta install program, and follow the instructions presented. The installer will ask for administrator authorization. Once Delta is installed and if so desired, double-click on the Manuals install program and follow the instructions presented. The installer will ask for administrator authorization. Eject the CD-ROM once the installation is complete.
Delta NMR Software Release Notes V5.0.4
6. Delta will need a license key after installation.
Use the [Options] → [License Key] menu to set the license key. If you already have a Delta License Key, there is no need to apply for a new one.
The current Delta License Key will continue to work. 7. Restart Delta after installing the license key and it is now ready for use.
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Known Issues
4.1
Solutions when Delta freezes There are two steps to solve the freeze trouble of Delta. a. Restart the Delta program on the workstation. b. Restart the Control program on the spectrometer. In many cases, the freeze trouble will be solved by only step a. This section explains below. • Procedure of step a and step b • The cases where you need to accomplish step b
4.1.1
Step a (Restart the Delta program on the workstation) Restart the Delta program on the workstation. 1. Select the [File]-[Quit] menu on the Delta Console window.
2.
The confirm dialog opens. Click the [OK] button on the confirm dialog. Quit the Delta program.
3. Double click a Delta icon to run the Delta program.
the spectrometer you wish to use is in the spectrometer list, you can connect to the Ifspectrometer, you can continue using it. If you cannot connect, go to the next page.
Delta NMR Software Release Notes V5.0.4
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If the spectrometer you want to use is not in the spectrometer list After restarting the Delta program on the workstation, if the spectrometer you want to use is not in the spectrometer list, it may be “blocked”.
Spectrometer is listed
What is “block”?
Spectrometer is not listed
The “block” function terminates the communication between the Delta program on the workstation and the control program on the spectrometer. Because the communication is often lost under the two cases below, it is no use monitoring the states of the spectrometer. • Where there is a spectrometer has a network address different from your NMR system (Cannot communicate with Delta you are using) on the same network. • Where the communication is often lost between the Delta and Control program by network problems such as physical network problems, wrong settings, and network traffic. Therefore, when the communication is often lost for the constant time, the Delta program blocks the spectrometer and stops communicating with it.
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Delta NMR Software Release Notes V5.0.4
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How to unblock
1. Select the [Tools]-[Service Manager] menu on the Delta Console window.
2. Check if the spectrometer you are using is listed under [Blocked Devices] at the bottom of the Service Manager view. The blocked devices are represented by the IP address.
Spectrometer is blocked
No spectrometer is blocked
the spectrometer you are using is blocked, go to step 3. IfIf the spectrometer you are using is not blocked, you need to restart the Control program on the spectrometer. Go to section 4.1.2 “Step b (Restart the Control program on the spectrometer)".
Delta NMR Software Release Notes V5.0.4
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3. Select the spectrometer you are using from [Blocked Devices], and click [Unblock Device] button.
① Select
② Click
Wait for a few seconds until it is displayed in the spectrometer list.
is in the spectrometer list on the Spectrometer Control window, Ifyouthecanspectrometer go ahead and operate the spectrometer. spectrometer is not in the spectrometer list on the Spectrometer Control window, Ifyoutheneed to restart the Control program. The instruction is section 4.1.2 “Step b (Restart the Control program on the spectrometer)”.
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Delta NMR Software Release Notes V5.0.4
4.1.2
Step b (Restart the Control program on the spectrometer) Restart the Control program on the spectrometer. Please quit the Delta program before restarting the Control program. 1. Select [All Programs]-[JEOL]-[Remote Maintenance Tool]-[Remote Maintenance Tool(Instrument)] from the Start menu.
2. Log in to [Remote Maintenance Tool(Instrument)] as “console”.
The password and the username are the same. Select the [Control Service Management] menu on Remote Maintenance Tool. 3.
4. Click the [RESTART Control Service] button.
If you check on the [Delete job related files] check box, all jobs and queues are deleted when the Control program is restarted.
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5. Click the [Yes] button.
When clicking the [Yes] button, the Control program is started restarting. In case the Control program has been already stopped At this time, the [Control Service Management] is displayed as “Control service is stopped”. Please click the [START Control Service] button to run the Control program.
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Delta NMR Software Release Notes V5.0.4
4.2
Memory leak and handle leak If Delta appears to extremely slow down after a long period of use, the available resources have decreased. • Memory leak Memory leak occurs when applications acquire memory but fails to release it to the operating system. It can diminish the performance of the computer by reducing the amount of available memory. • Handle leak Handle leak occurs when applications acquire handles such as information of file opened, memory shared by several applications, and so on but fails to release them to the operating system. ●
If Delta appears to extremely slow down Please restart the Delta program on the workstation and/or the Control program on the spectrometer. This will release the memories and handles used by Delta, and restore the normal operating speed. You need not restart the workstation and spectrometer. We recommend restarting the Delta and Control program regularly.
How to restart the Delta program (Workstation) After finishing the measurement and data processing, please quit the Delta program. Instruction how to restart the Delta program is section 4.1.1 “Step a (Restart the Delta program on the workstation)”. How to restart the Control program (Spectrometer) Refer to section 4.1.2 “Step b (Restart the Control program on the spectrometer)”. Please quit the Delta program on the workstation before restarting the Control program.
Delta NMR Software Release Notes V5.0.4
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4.3
Gradient shim is not run This section explains how to solve the trouble parameters of gradient shim are NULL or blacked out. Phenomenon • Gradient shim is not running in spite of executing it. • The error message is not displayed on Spectrometer Control window. • When opening the Gradient Shimming tool, the values of parameters are NULL or the input boxes are blacked out. Cause Delta fails to store values of parameters of gradient shim.
The values of parameters are NULL
The parameters set to NULL are random.
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Delta NMR Software Release Notes V5.0.4
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How to check and solve the trouble
1. Invoke the Gradient Shimming tool.
2. Check parameters of the Gradient Shimming tool. ① The [Shim Set] is masked
are no calibration maps under the selected condition. There Please check whether the [System Type], [Nucleus], [Solvent] are correct or not. If correct, you need to measure calibration maps under the condition. ② The [Shim set] is not checked
Check on the [Shim Set] check box you want to perform shimming
③ The values of parameters are NULL or the input boxes are blacked out
need to restart the Control program on the spectrometer. The instruction is You section 4.1.2 “Step b (Restart the Control program on the spectrometer)”.
Delta NMR Software Release Notes V5.0.4
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4.4
Resolution is bad when gradient shim is measured Parameters of gradient shimming have been changed to make the measurement duration time to run shorter since Delta V5.0.2. • Until Delta V5.0.1 You can obtain good resolution but it takes time to measure gradient shimming. • Since Delta V5.0.2 You can obtain reasonable resolution and it takes less time to measure gradient shimming. Parameter
Default 4 (V5.0.1) → 2 (V5.0.2)
Scans
Relax Delay
Condition Nucleus is 2H and Solvent is Acetone-D6，Benzene-D6， D2O，DMSO-D6，or Tetrahydrofuran-D8
4 (Not changed)
Other solvents
5 (V5.0.1) → 1［s］ (V5.0.2)
Nucleus is 2H.
5［s］(Not changed)
Other nuclei
2 (Not changed)
All solvents
Iterations
◇CAUTION◇ If you cannot obtain resolution you want, please think of changing the above parameters. When you change them, you need to check off the [For this sample only] check box and then change the above parameters. ・ If the [For this sample only] is checked off When you change shimming parameters (Tip Angle, Scans, …), the changes will be applied for all samples. ・ If the [For this sample only] is checked on When you change shimming parameters (Tip Angle, Scans, …), the changes will be applied only for the current sample definition.
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Delta NMR Software Release Notes V5.0.4
4.5
How to update the [Parameter Bar] at the Spectrometer Control window If the values of the [Parameter Bar] at the Spectrometer Control window are not updated, please log in to the spectrometer again. This will update the values on the Parameter Bar.
Parameter Bar
1. Click the [Disconnect from the spectrometer] button.
2. Click the [Yes] button.
3. Connect to the spectrometer again.
The information of the [Parameter bar] is updated.
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4.6
Measurements are automatically run upon restarting the spectrometer side As shown in the picture below, if the Control program or spectrometer is restarting while a job remains on the Queue, the system will automatically start measurement upon being restarted. To avoid this, you need to delete all queues before restarting them. The job currently measuring is not automatically run upon being restarted.
Job#66 is being measured. It is not automatically measured upon being restarted. Job#67 and Job#68 are automatically measured upon being restarted. 5
Changes in Delta V5.0.4
5.1
Changes summary Category
5.2
Item
1
Instrument support
New Auto Sample Changer is supported
2
Processing
An issue with a parameter of Shear(phase_x_y) process was fixed
3
Probe tuning
The control flow of AUTO TUNING UNIT was improved
4
Operation
Issues of memory leaks were improved and freezes were fixed
5
Operation
The display format of [Update Job] pane was fixed
6
Gradient shim
An issue with [Calculate] check box of [Recvr Gain] parameter was fixed
7
Pulse sequence
Additional pulse sequences added
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Pulse sequence
Pulse sequences were updated
Details of changes ① New AUTO SAMPLE CHANGER is supported The slot number of new Auto Sample Changer is 30 or 64 or 100.
ASC30, ASC64, ASC100 displayed on Delta (Figure shows sample with slot 1 is loaded)
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Delta NMR Software Release Notes V5.0.4
② An issue with Shear(phase_x_y) process was fixed Shear(phase_x_y) used in MQMAS process was fixed to be able to change “alpha” parameter.
③ The control feature of AUTO TUNING UNIT was improved The stability of AUTO TUNING UNIT has been improved. ④ Issues of memory leaks were improved and freezes were fixed Memory leaks have been improved, and the programs have been fixed so that it does not freeze freezes in the following operations. • The update processes of the parameter bar could cause freeze of Delta program. • When you copy a spectrum on the monitor tab, Delta program could freeze. • When update processes of the data server on the spectrometer are simultaneously executed by more than one thread, Control program could freeze. ⑤ The display format of [Update Job] pane was fixed When measurement time of Job is “0:00”, the Job name and the measurement time has been changed to separate by space.
V503
Delta NMR Software Release Notes V5.0.4
V504
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⑥ An issue with [Calculate] check box of [Recvr Gain] parameter was fixed When you check off [For this sample only] check box and then change the value of [Calculate] check box of [Recvr Gain] parameter, the change of [Calculate] should have been applied to another sample. This has been fixed on Delta V5.0.4.
Gradient Shimming Tool ⑦ Additional pulse sequences added Refer to section 5.3 “Additional pulse sequences” for detail. ⑧ Pulse sequences were updated a. sat_transfer_difference b. sat_transfer_difference_wgh • Changed number of points to sample (x_points) from 4096 to 8192. • Changed selectively irradiation offset (std_sel_onreso, std_sel_offreso) from (30ppm, -0.4ppm) to (0.5ppm, -10ppm). • Fixed the problem that the difference between signal selectively irradiated for on-resonance and off-resonance cannot be obtained correctly. c. inadequate_2d d. inadequate_2d_dept e. inadequate_2d_dept_pfg f. inadequate_2d_inept_si g. inadequate_2d_jcp_pfg h. inadequate_2d_pfg i. inadequate_2d_phase • Changed number of points to sample (x_points) from 4096 to 8192. • Changed observation range of the indirect dimension (y_sweep) to twice as much as that of direct dimension (x_sweep). cpmas_spin_echo_t2 j. • Fixed the execution block in the Pulse section. k. waltz • Changed the WALTZ default scheme from WALTZ-16 to WALTZ-65 to decrease the decoupling sideband.
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Delta NMR Software Release Notes V5.0.4
5.3
Additional pulse sequences
5.3.1
single_pulse_wet_180_slp
■ Purpose
This pulse sequence is used to measure the spectrum of a sample with a single pulse while eliminating the solvent signal. ■ Outline
This performs the single pulse measurement with the eliminating of the solvent signal by WET solvent pulse. Compared with single_pulse_wet_slp measurement method, this improves residual water suppression, clean spectral phase properties, and good signal intensity retension. ■ Pulse sequence diagram
[x_domain]
[x_pulse]×4
[wet_pulse] [wet_pulse] [wet_pulse] [wet_pulse] [relaxation _delay]
[x_atn] [acq_time]
[irr_atn_dec]
[irr_domain] PFG1
[wet_grad_amp] PFG2
[wet_grad_amp]/2 [wet_grad_amp]/4 [wet_grad_amp]/8
PFG3
PFG4
FG Channel
■ Extended sequences Extended sequence
Description
Default
dante_presat
Specify the performance of the dante pre-saturation
FALSE
tri_mode
Specify the second irradiation mode. Select either Off, Presaturation, or Homo Decouple
Off
■ Parameters Parameters
Description
Default
x_domain
Observation nucleus
Proton
x_offset
Observation center
5 ppm
x_sweep
Observation range
20 ppm
x_points
Number of points to sample
32768
scans
Number of scans to accumulate
8
x_prescans
Number of pre-accumulations (dummy scans)
4
x_pulse
90° pulse width in the observation channel (1H)
x90 set in the probe file
x_atn
Value of the attenuator that specifies the output level of the RF pulse in the observation channel. With every additional 6dB, the necessary pulse width doubles.
xatn set in the probe file
composite_pulse
Use of the composite pulse
FALSE
relaxation_delay
Waiting time between repeated pulses
5.0 s
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Parameters
Description
Default
repetition_time
relaxation_delay + x_acq_time is delayed.
wet_pulse
Pulse width of the shaped pulse used in the WET sequence
x90_soft set in the probe file
wet_atn
RF output level of the shaped pulse used in the WET sequence. With every additional 6dB, the necessary pulse width doubles.
xatn_soft set in the probe file
wet_shape
Waveform of the shaped pulse
GAUSS
wet180
Selects WET180 solvent pulse or standard WET solvent pulse.
TRUE
wet_number
Number of peaks to be irradiated with WET
1
wet_offset1
Resonance position of the peak to be irradiated with WET
5 ppm
wet_offset2
Resonance position of the peak when two or more peaks are irradiated with WET
0 ppm
wet_offset3
Resonance position of the peak when two or more peaks are irradiated with WET
0 ppm
wet_offset4
Resonance position of the peak when two or more peaks are irradiated with WET
0 ppm
wet_offset5
Resonance position of the peak when two or more peaks are irradiated with WET
0 ppm
wet_offset6
Resonance position of the peak when two or more peaks are irradiated with WET
0 ppm
wet_slp
Displays the WET irradiation positions.
wet_grad
Width of the PFG pulse
2 ms
wet_grad_amp
Output level of the PFG pulse
0.144 T/m
wet_grad_shape
Waveform of the PFG pulse
SINE
wet_grad_recover
Recovery time after PFG pulse
0.1 ms
irr_domain
Irradiation nucleus
Carbon13
irr_offset
Resonance position of the irradiation peak
70 ppm
irr_pwidth
Pulse width of the decoupling pulse
irr90_hi set in the probe file
irr_noise
Decoupling mode
GARP
irr_atn_dec
RF output level for decoupling. Every time 3dB is added, the RF output is halved.
Irratn_hi set in the probe file
lock_hold
Stops the lock signal sampling
FALSE
■ Category
lc nmr, 1D, liquids, Single_pulse, Water_Suppression ■ Process List
proton.list ■ Supplementary notes
WET is the abbreviation of Water suppression Enhanced through T effects. 1
WET180 is a better sequence for suppressing water signal than the standard WET. S.H.Smallcombe, S.L.Patt, P.A.Keifer, J.Magn.Reson., 117A, 295-303(1995)
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Delta NMR Software Release Notes V5.0.4
5.3.2
std_tocsy_pfg_phase_pn
■ Purpose
This pulse sequence is used to analyze interaction between protein and ligands. ■ Outline The difference between a saturation transfer- and a normal-NMR spectrum provides a STD-TOCSY spectrum. Ligands only that possess binding-activity to protein can be observed. ■ Pulse sequence diagram [x_pulse] [STD_sel_180] 90° [x_domain]
[relaxation_ delay] STD_sel_shape STD_sel_atn STD_sel_onreso
[x_pulse] [STD_sel_180] 90° [mix_time]
t1
phase_acq [relaxation_ delay]
MLEV17
[trim]
[grad_1]
STD_sel_shape STD_sel_atn STD_sel_offreso
[trim]
[grad_2]
[mix_time]
t1
phase_acq
MLEV17
[trim]
[grad_1]
[trim]
[grad_2]
FG Channel
■ Extended sequences Extended sequence
Description
Default
dante_presat
Specify the performance of the dante pre-saturation
FALSE
irr_mode
Specify the second irradiation mode. Select either Off, Presaturation, or Homo Decouple Specify the second irradiation mode. Select either Off, Presaturation, or Homo Decouple
Off
Specify the performance of the Spin lock purge pulse
FALSE
tri_mode t1p_pfilter
Off
This is used to suppress protein signals.
■ Parameters Parameters
Description
Default
x_domain
Observation nucleus
Proton
x_offset
Observation center
5 ppm
x_sweep
Observation range
15 ppm
x_points
Number of points to sample
2048
scans
Number of scans to accumulate
4
x_prescans
Number of pre-accumulations (dummy scans)
4
x_pulse
90° pulse width in the observation channel (1H)
x90 set in the probe file
x_atn
Value of the attenuator that specifies the output level of the RF pulse in the observation channel. With every additional 6dB, the necessary pulse width doubles.
xatn set in the probe file
y_points
Number of points to sample on the t1 axis
128
Delta NMR Software Release Notes V5.0.4
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Parameters
Description
Default
std_sel_180
180° pulse width of the selection excitation pulse
Two times x90_soft set in the probe file
std_sel_atn
RF output level of the selective excitation pulse. With every additional 6dB, the necessary pulse width doubles.
xatn_soft set in the probe file
std_sel_onreso
Resonance position of the peak to be selectively irradiated
0.5 ppm
std_sel_offreso
Irradiation position for off-resonance
-10 ppm
std_sel_shape
Waveform of the selective excitation pulse
GAUSS
std_loop
Number of the selective excited pulses
40
saturation_time
The total time of selective excitation pulse
std_sel_180× std_loop
x_spinlock_pulse
90°pulse width of the spin lock pulse
x90_spin set in the probe file
x_spinlock_atn
RF output level of the spin lock pulse
xatn_spin set in the probe file
trim
Pulse width of the trim pulse
2.5 ms
mix_time
Spin lock mixing time
50 ms
mix_time_loop
Displays number of irradiation of the spin lock pulse
total_mix_time
Displays accurate mixing time
grad_1
Pulse width of the first FG pulse (PFG1)
1 ms
grad_1_amp
Output level of the first FG pulse (PFG1)
0.09 T/m
grad_2
Pulse width of the second FG pulse (PFG2)
grad_1
grad_2_amp
Output level of the second FG pulse (PFG2)
grad_1_amp
grad_shape
Waveform of the PFG pulse
SINE
grad_recover
Recovery time after PFG pulse
0.1 ms
relaxation_delay
Waiting time between repeated pulses
2.0 s
repetition_time
relaxation_delay + x_acq_time + saturation_time is delayed.
■ Category
2D, noe, liquids ■ Process list file 2d_homo2d_pn.list ■ How to interpret the spectrum
Ligands only that possess binding-activity to protein can be observed
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Delta NMR Software Release Notes V5.0.4
5.3.3
std_tocsy_wgh_pfg_phase_pn
■ Purpose
This pulse sequence is used for analyzing interaction between protein and ligands. ■ Outline A STD-TOCSY pulse sequence with WATERGATE water suppression. ■ Pulse sequence diagram [x_pulse] [STD_sel_180] 90° [x_domain]
[relaxation_ delay] STD_sel_shape STD_sel_atn STD_sel_onreso
W5 [mix_time]
t1
phase_acq [relaxation_ delay]
MLEV17
[trim]
[grad_1]
[x_pulse] [STD_sel_180] 90°
W5
[trim]
t1
STD_sel_shape STD_sel_atn STD_sel_offreso
phase_wgh2 [grad_2] [wgh_grd]
W5
W5
[mix_time]
phase_acq
MLEV17
[trim]
[trim]
[grad_1]
phase_wgh2 [grad_2]
[wgh_grd]
FG Channel
■ Extended sequences Extended sequence
Description
Default
dante_presat
Specify the performance of the dante pre-saturation
FALSE
irr_mode
Specify the second irradiation mode. Select either Off, Presaturation, or Homo Decouple Specify the second irradiation mode. Select either Off, Presaturation, or Homo Decouple
Off
Specify the performance of the Spin lock purge pulse
FALSE
tri_mode t1p_pfilter
Off
This is used to suppress protein signals.
■ Parameters Parameters
Description
Default
x_domain
Observation nucleus
Proton
x_offset
Observation center
5 ppm
x_sweep
Observation range
15 ppm
x_points
Number of points to sample
2048
scans
Number of scans to accumulate
4
x_prescans
Number of pre-accumulations (dummy scans)
4
x_pulse
90° pulse width in the observation channel (1H)
x90 set in the probe file
x_atn
Value of the attenuator that specifies the output level of the RF pulse in the observation channel. With every additional 6dB, the necessary pulse width doubles.
xatn set in the probe file
y_points
Number of points to sample on the t1 axis
128
std_sel_180
180° pulse width of the selection excitation pulse
Two times x90_soft set in the probe file
std_sel_atn
RF output level of the selective excitation pulse. With every additional 6dB, the necessary pulse width doubles.
xatn_soft set in the probe file
Delta NMR Software Release Notes V5.0.4
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Parameters
Description
Default
std_sel_onreso
Resonance position of the peak to be selectively irradiated
0.5 ppm
std_sel_offreso
Irradiation position for off-resonance
-10 ppm
std_sel_shape
Waveform of the selective excitation pulse
GAUSS
std_loop
Number of the selective excited pulses
40
saturation_time
The total time of selective excitation pulse
std_sel_180× std_loop
x_spinlock_pulse
90°pulse width of the spin lock pulse
x90_spin set in the probe file
x_spinlock_atn
RF output level of the spin lock pulse
xatn_spin set in the probe file
trim
Pulse width of the trim pulse
2.5 ms
mix_time
Spin lock mixing time
50 ms
mix_time_loop
Displays number of irradiation of the spin lock pulse
total_mix_time
Displays accurate mixing time
grad_1
Pulse width of the first FG pulse (PFG1)
1 ms
grad_1_amp
Output level of the first FG pulse (PFG1)
0.09 T/m
grad_2
Pulse width of the second FG pulse (PFG2)
grad_1
grad_2_amp
Output level of the second FG pulse (PFG2)
grad_1_amp
grad_shape
Waveform of the PFG pulse
SINE
grad_recover
Recovery time after PFG pulse
0.1 ms
watergate_selection
Excitation characteristics of the WATERGATE pulses
W5
Pulse width of the WATERGATE pulse
x90 set in the probe file
Signal excitation range of WATERGATE. Set it to the wider frequency range to cover the range from the observation center to its edge
5000 Hz
wgh_null wgh_tau
Pulse interval of the WATERGATE pulses is displayed.
1/wgh_null
wgh_grad
Pulse width of the FG pulse for WATERGATE
1 ms
wgh_grad_amp
Output level of the FG pulse for WATERGATE
0.12 T/m
wgh_grad_shape
Waveform of the FG pulse for WATERGATE
SQUARE
wgh_grad_recover
Recovery time after the FG pulse for WATERGATER
0.1 ms
relaxation_delay
Waiting time between repeated pulses
2.0 s
repetition_time
relaxation_delay + x_acq_time + saturation_time is delayed.
wgh_x_pulse
■ Category
2D, noe, liquids ■ Process list file 2d_homo2d_pn.list ■ How to interpret the spectrum
Ligands only that possess binding-activity to protein can be observed
22
Delta NMR Software Release Notes V5.0.4
5.3.4
waterlogsy
■ Purpose
This pulse sequence is used for analyzing interaction between protein and ligands. ■ Outline The water magnetization is transferred via the protein to ligands. The resonances of non-binding compounds appear with negative signals, whereas binding compounds appear with positive signals. ■ Pulse sequence diagram W5
[obs_sel_180]
phase_acq
[mix_time]
[x_domain] [relaxation_ delay]
W5
obs_sel_180_shape phase_shape_1 obs_sel_180_atn
phase_wgh2 [grad_3] [grad_4]
[grad_1]
[mix_time]
FG Channel
■ Extended sequences
Not used. ■ Parameters Parameters
Description
Default
x_domain
Observation nucleus
Proton
x_offset
Observation center
5 ppm
x_sweep
Observation range
15 ppm
x_points
Number of points to sample
8192
scans
Number of scans to accumulate
16
x_prescans
Number of pre-accumulations (dummy scans)
4
mod_return
Number of transfers of data
1
x_pulse
90° pulse width in the observation channel (1H)
x90 set in the probe file
x_atn
Value of the attenuator that specifies the output level of the RF pulse in the observation channel. With every additional 6dB, the necessary pulse width doubles.
xatn set in the probe file
obs_sel_180
180° pulse width of the selection excitation pulse
Two times x90_soft set in the probe file
obs_sel_180_atn
Value of the attenuator that specifies the output level of the RF pulse
Xatn_soft set in the probe file
obs_sel_shape
Waveform of the selective excitation pulse
REBURP
watergate_selection
Excitation characteristics of WATERGATE pulses
W5
Pulse width of the WATERGATE pulse
x90 set in the probe file
wgh_x_pulse
Delta NMR Software Release Notes V5.0.4
23
Parameters
Description
Default 2500 Hz
wgh_null
Signal excitation range of WATERGATE. Set it to the wider frequency range to cover the range from the observation center to its edge
wgh_tau
Pulse interval of the WATERGATE pulses is displayed.
1/wgh_null
mix_time
Mixing time of WaterLOGSY
1000 ms
relaxation_delay
Waiting time between repeated pulses
5.0 s
repetition_time
relaxation_delay + x_acq_time is delayed.
grad_1
Pulse width of the first FG pulse (PFG1)
1 ms
grad_1_amp
Pulse output level of the first FG pulse (PFG1)
0.04 T/m
grad_2_amp
Pulse output level of the second FG pulse (PFG2)
0.005 T/m
grad_3
Pulse width of the third FG pulse (PFG3)
1 ms
grad_3_amp
Pulse output level of the third FG pulse (PFG3)
0.102 T/m
grad_4
Pulse width of the fourth FG pulse (PFG4)
1 ms
grad_4_amp
Pulse output level of the fourth FG pulse (PFG4)
0.066 T/m
grad_shape
Waveform of the FG pulse. Select the waveform from GAUSS, SINE, or SQUARE
SINE
grad_recover
Recovery time after the FG pulse
0.1 ms
lock_hold
Hold lock level when FG pulse running
TRUE
■ Category
1D, noe, liquids, Water_Suppression ■ Process list file
proton.list ■ How to interpret the spectrum Non-binding compounds appear with negative signals, whereas binding compounds appear with positive signals.
24
Delta NMR Software Release Notes V5.0.4
5.3.5
waterlogsy_wf
■ Purpose
This pulse sequence is used for analyzing interaction between protein and ligands. ■ Outline Waterlogsy pulse sequence that a water-flipback pulse is added. ■ Pulse sequence diagram W5
[obs_sel_180]
phase_acq
[mix_time]
[x_domain] [relaxation_ delay]
W5
obs_sel_180_shape phase_shape_1 obs_sel_180_atn
phase_shape2
phase_wgh2
[grad_3] [grad_4]
[grad_1]
[mix_time]
FG Channel
■ Extended sequences Extended sequence relaxation_filter
Description Specify the relaxation filter from Off, T2 Filter, T1p Filter.
Default Off
■ Parameters Parameters
Description
Default
x_domain
Observation nucleus
Proton
x_offset
Observation center
5 ppm
x_sweep
Observation range
15 ppm
x_points
Number of points to sample
8192
scans
Number of scans to accumulate
16
x_prescans
Number of pre-accumulations (dummy scans)
4
mod_return
Number of transfers of data
1
x_pulse
90° pulse width in the observation channel (1H)
x90 set in the probe file
x_atn
Value of the attenuator that specifies the output level of the RF pulse in the observation channel. With every additional 6dB, the necessary pulse width doubles.
xatn set in the probe file
obs_sel_180
180° pulse width of the selection excitation pulse
20 ms
obs_sel_180_atn
Value of the attenuator that specifies the output level of the RF pulse
40 dB
obs_sel_180_shape
Waveform of the selective excitation pulse
REBURP
obs_sel_180_offset
Resonance position of the peak to be selectively irradiated
x_offset
obs_sel_90
90° pulse width of the selection excitation pulse
x90_soft set in the probe file
obs_sel_90_atn
Value of the attenuator that specifies the output level of the RF pulse
xatn_soft set in the probe file
Delta NMR Software Release Notes V5.0.4
25
Parameters
Description
Default
obs_sel_90_shape
Waveform of the selective excitation pulse
GAUSS
obs_sel_90_offset
Resonance position of the peak to be selectively irradiated
x_offset
watergate_selection
Excitation characteristics of WATERGATE pulses
W5
Pulse width of the WATERGATE pulse
x90 set in the probe file
wgh_x_pulse wgh_null
Signal excitation range of WATERGATE. Set it to the wider frequency range to cover the range from the observation center to its edge
2500 Hz
wgh_tau
Pulse interval of the WATERGATE pulses is displayed.
1/wgh_null
mix_time
Mixing time of WaterLOGSY
1000 ms
relaxation_delay
Waiting time between repeated pulses
5.0 s
repetition_time
relaxation_delay + x_acq_time is delayed.
grad_1
Pulse width of the first FG pulse (PFG1)
1 ms
grad_1_amp
Pulse output level of the first FG pulse (PFG1)
0.04 T/m
grad_2_amp
Pulse output level of the second FG pulse (PFG2)
0.005 T/m
grad_3
Pulse width of the third FG pulse (PFG3)
1 ms
grad_3_amp
Pulse output level of the third FG pulse (PFG3)
0.102 T/m
grad_4
Pulse width of the fourth FG pulse (PFG4)
1 ms
grad_4_amp
Pulse output level of the fourth FG pulse (PFG4)
0.066 T/m
grad_recover
Waveform of the FG pulse. Select the waveform from GAUSS, SINE, or SQUARE Recovery time after the FG pulse
lock_hold
Hold lock level when FG pulse running
TRUE
relaxation_filter
Specify the relaxation filter from Off, T2 Filter, T1p Filter.
Off
delay_list
In case relaxation_filter = T2 Filter Irradiation time of the CPMG pulse
1.0 s
tau_step
In case relaxation_filter = T2 Filter Pulse interval (2τ) of the CPMG pulse
200 ms
tau_interval_t2
In case relaxation_filter = T2 Filter Displays τ of the CPMG pulse sequence
(tau_step x_pulse×2)/2
grad_shape
loop_number t1pfilter_time t1pfilter_atn
In case relaxation_filter = T2 Filter Number of the 180° pulses determined by delay_list and tau_step In case relaxation_filter = T1p Filter Pulse width of the purge pulse In case relaxation_filter = T1p Filter Attenuator value of the purge pulse. With every additional 6dB, the necessary pulse width doubles.
SINE 0.1 ms
100 ms xatn_spin set in the probe file
■ Category
1D, noe, liquids, Water_Suppression ■ Process list file proton.list
26
Delta NMR Software Release Notes V5.0.4
■ How to interpret the spectrum
Non-binding compounds appear with negative signals, whereas binding compounds appear with positive signals.
Delta NMR Software Release Notes V5.0.4
27
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