In its simplest form, an AU macro defines one XWIN-NMR command. For example the macros ZG and FT execute the X WIN-NMR commands zg and ft, respectively. Other macros like FETCHPAR and IEXPNO do not define XWIN-NMR commands, their function is only relevant in the context of an AU program. Hi, I wanna Brukers TopSpin/XWIN-NMR to log the start and end times of every experiment. With this information I can. Posted: oxy 31 Aug 28 '19 at 01:42.
- SampleTrack supports all the AVANCE™ series spectrometers which utilize XWIN-NMR™ 3.1 patch level 11 or higher or TopSpin ® 1.2 or higher. SampleTrack's automation interface for spectrometers is built on the IconNMR™ platform. Within IconNMR all orders from SampleTrack are executed automatically.
- Modules which can be started from XWIN-NMR. 2.1 The XWIN-NMR module versions of XWIN-PLOT and AUTOPLOT If started from within XWIN-NMR, XWIN-PLOT and AUTOPLOT automatically load the current data set and a layout that is specified by setting the XWIN-NMR LAY-OUT parameter. To set this layout parameter, you can use the X WIN-NMR command edo.
- The XWIN-NMR screen offers a wide variety of functions, many of which are self- explanatory, such as expansion of region, moving spectrum up, down, left, right, etc. Expanding a particular region – you can expand a particular portion of the spectrum. To do that, click.
Release Letter 3.1
Chapter 8. Bugs corrected in NMR-SUITE 3.1
Chapter 8. Bugs corrected in NMR-SUITE 3.1
8.1 XWIN-NMR 3.1
8.1.1 Acquisition
1. Bug 2740: Sometimes after start of gs the acquisition window shows invalid FID, and it may take a few minutes until the correct FID is displayed. This happens reliably using a PC with P3 faster than 700MHz and when td is larger than 20k.
2. Bug 2727: Sometimes samples are not inserted during SampleRail automation, but the message: 'Sample missing (can’t lock)' is displayed and the run is aborted.
3. Bug 2682: When cortab is done for 1H as the first preamplifier module below the Cover module of an HPPR2, the results can be very poor.
4. Bug 2672: If the new edprosol command imports old prosol parameters, then the old D_grad pulse is imported in seconds instead of usec.
5. Bug 2671: 1) In 1D experiments writing to file #0, #1 etc fails except for the last written file. Files are produced correctly but are removed after termination of the experiment. 2) In 2D experiments this error didn’t occur, but it was impossible to write to #1 etc if #0 was not written first. 3) Under WINNT or WIN2000 #1 always fails with error message 'illegal file name'
6. Bug 2639: In case of a BBI and BBO probes with ATMA accessory the probe firmware (PICS) could be damaged when two simultaneous atma commands are active. This occasionally happens because the atma command is not terminated correctly when stop is done manually. Therefore, the atma command has to be terminated explicitly with the kill command. When atma is done during an automation procedure no problems occured up to now.
7. Bug 2638: If during gs the frequency is changed several MHz on an Avance spectrometer equipped with AQS rack the signal may disappear.
8. Bug 2625: You can select each nucleus of an ATMA broadband probe only once. The second time the following error will be shown: 'Error: bb-channel can’t be set to f1 [13C] <Probe-NucBB-MotorBase:movePreseted-Motor-Nr:9 <BB Tune>:can’t move to position -xxxx (-xx)>'.
9. Bug 2617: If a cpd program uses shaped pulses instead of rectangular pulses, the phases specified with #setphase and :0 after the shaped pulses are not executed correctly.
10. Bug 2602: The pulsdisp window shows no pulses in the CH1/CH2/.. window rows if the simulated spectrometer is equipped with a TCU3.
11. Bug 2595: HPPR2: When edhead is started and a probe without PICS is con-nected, the program crashes with an 'Illegal Termination of xxx process due to signal 6 - core dumped' message.
12. Bug 2586: If you have an aqcquisition running, then stop it and immediately start a new acquisition, it can happen that the new acquisition aborts with the error message: 'Cannot <do something>: timeout (device sleeping, off or not connected)'.
13. Bug 2584: atma and atmm fails with the error message 'frequency out of range' on an 600MHz AV spectrometer for 1H nuclei. Adobe acrobat x pro free trial.
14. Bug 2572: Sweep width for homodecoupling is wrong by a few percent
15. Bug 2544: When using the HPPR2 it can happen that different modules are erroneously recognized as identical modules.
16. Bug 2454: Sometimes the lock gets into a tri state, i.e.1) un-locked press lock button 2) semi-locked: lock display looks locked, but lock LED is blinking press lock button 3) locked press lock button again get back to state 1). If the BSMS reached that state, this behaviour is reproducible.
17. Bug 2437: The rsh command gives error messages: Warning: 'ShimFile ’/u/exp/stan/nmr/lists/bsms/****’ was not stored with the same Probe'
8.1.2 Processing
1. Bug 2700: The edp command shows in the F1 column, depending on AQORDER, for 2D slices of 3D dataset wrong parameters. The same applies to dpp and lpp. The single parameters which have relations between proc and acqu parameters show the same behaviour.
2. Bug 2653: The nmrquant command doesn’t work properly in XWIN-NMR 3.0 under Windows, because the basereg file is not created.
3. Bug 2631: On processed 2D datasets with total size equal or less 1024 points(e.q. SI{F2} x SI{F1} = 32 x 32) the command dosy2d may not work but issue the error message: 'Can not get a 4096 bytes shared memory for processing with SMX-size given from this processed dataset. Call your system administrator to check tunable OS parameter SHMMAX.'X
4. Bug 2614: wpar/rpar is unable to read/write the parameter files dosy and t1par.
5. Bug 2592: Sometimes, the deconvolution command ldcon (but it could also happen for gdcon) terminates with 'segmentation violation' and no fitting is done.
6. Bug 2591: sinocal never uses the default values specified at the beginning of the AU program. Instead, if the spectrum type cannot be detected from the dataset name, the values for the water suppression experiment are used.
7. Bug 2590: Depending on the noise level of the 2D spectrum, the AU program pp2dmi sometimes doesn’t find any peaks.
8. Bug 2566: 2D processing commands like ’xf2p’ may finish immediately without an error message. The entry in the history file shows a -1 status like: 'cmd term: xf2p; status=-1'. After this the graphics program does not display the processed data any longer because 2D processing sets the dsp.hdr file entry ##LOC= -2.
9. Bug 2545: The input filename of fromjdx is truncated to 40 characters, the out-put in tojdx to 65 characters which is too small on WinNT.
8.1.3 Display
1. Bug 2611: xcpu dies with with following message:'Graphic restart after normal error in ’xlib’, xerror of failed request:bad value ( or bad match )..CPR: graphic server called exit (1)'. The installation of ’VNMR’ or ’MathLab’ may set the X server to 12-bit PseudoColor as default Visual and therefore cause this error.
2. Bug 2478: After an update of a Linux Workstation used as display for XWIN-NMR to Suse-7.0 or RedHat-7.0 the XWIN-NMR menues don’t show properly. In eda only the editable fields are readable, other text is shown as squareblocks.
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3. Bug 1993: The T1 information about the fitted peak as it is displayed on the screen in the little Info window is inconsistent with what is written to the output files (also on the screen). This happens when the baseline points (baslpnts) file is not written in strictly descending order. That means, highest ppm values first.
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NMR Software and Manuals
Academic-LiscenceSoftware |
Lastupdated May, 2004
Xwin Media Trans
BRUKER Software (Commercial) liscenced to the Wolfson Centre:Program | Online Manual | Brief Description |
XWINNMR | XWINNMR Manual | XWIN-NMRis the operating software for our spectrometer. All acquisition andprocessing is performed using this software. Access to the manualrequires free registration, or you can find a hardcopy at the NMR Laboratory. |
AURELIA | AURELIAManual | AURELIA isused for the display, plotting and semi-automated analysis of 2D, 3D and4D NMR datasets (J. Biomol. NMR, 6, 255-270, 1995). Access to themanual requires free registration, or you can find a hardcopy at the NMR Laboratory. |
XWIN-PLOT | XWIN-PLOTManual | XWIN-PLOTcreates printouts of NMR data, including NMR spectra and otherNMR-related data. XWIN-PLOT is an easy-to-use, object-oriented toolworking on a What You See Is What You Get basis. Access to the manualrequires free registration, or you can find a hardcopy at the NMR Laboratory. |
Win Nmap
Xwin Mobax
Academic-liscenced Software:
Xwinmart
PROGRAM | Online Manual | Brief Description |
XPLOR | XPLOR Manual | X-PLOR is a program system for computational structuralbiology. X-PLOR explors the conformational space of macromoleculesrestrained to regions allowed by combinations of empirical energyfunctions and experimental data. |
MOLMOL | MolMolManual | MOLMOL is a molecular graphics program for displaying,analyzing, and manipulating the three-dimensional structure ofbiological macromolecules, with special emphasis on the study of proteinor DNA structures determined by NMR. |
GRASP | Grasp Manual | GRASP is a molecular visualization and analysis program. Itis particularly useful for displaying and manipulating molecularsurfaces electrostatic properties. |
MARDIGRAS | MardigrasManual | MARDIGRAS is a program for calculating proton-protondistances and error bounds from cross-peak intensities measured from a2D NOESY spectrum. It algorithm converts the intensity matrix(non-observable intensities are supplied from a model) to a relaxation rate matrix, which is improved by an iterative procedure. |
SPARKY | SPARKYManual | Sparky displays processed NMR spectra. You can pick, assign,and integrate peaks using a graphical interface. You can work with anynumber of 2, 3 or 4 dimensional spectra simultaneously. The program hasbeen developed to assist in structure determination of proteins, DNA and RNA. |
CORMA | CormaManual | CORMA is a program for calculating the dipole-dipolerelaxation matrix for a system of protons and converting the matrix tointensities expected for a 2D-NOE experiment. |
PROCHECK | PROCHECKManual | Checks the stereochemical quality of a protein structure,producing a number of PostScript plots analysing its overall and residue-by-residue geometry. |
DelPhi | DelPhi Manual | DelPhi calculates the electrostatic potential in and arounda molecular system, using a finite difference solution to thePoisson-Boltzmann equation. It can be used to investigate electrostaticfields in a variety of molecular systems. |
XPLO2D | XPLO2DManual | This program performs several utility functions having to dowith the input or output of X-PLOR. Used here to add hydrogens to stripped PDB files. |
ISIS (MDL) | ISISManual | ISIS is a chemical drawing program distributed by MDL that produces WINDOWS-compatiblefigures. |