Delta Software For Nmr Database
25.10.2019by admin
Bio-Rad is a world leader in spectral data and software. The catalog below provides an overview of the IR, Raman, NMR, MS, UV-Vis spectral databases and KnowItAll™ KnowItAll ® Spectroscopy Software for spectral identification, database building, management, search, analysis, prediction, chemometics, structure drawing, and reporting. PERCH NMR Software quantum mechanical spectral analysis, structure verification, quantification rNMR - an open source software package written for the R statistical software. RNMR is designed to simplify the repetitive resonance assignment and quantification tasks associated with metabolomics. Sparky - NMR Assignment Program.
Delta Group Links: Supplier Registration. This service helps you access your preferred product-oriented materials like brochures, product manuals, software upgrades, and more. You could simply search our database by selecting product category or document type, or entering a product name directly.
Networked NMR Network Processing of NMR Data. These notes cover the following topics: Desktop NMR data processing. There is also a quick summary of: Last updated February 2004. For NMR data. The 300MHz Bruker system issues date-related filenames to users, which are printed on peak listings.
Similar date-based names are used for the 400MHz files. The older Bruker systems use DOS-like filenames in the format text.number, where number is 000 to 999, but these are not available over the network routinely.
Users of the JEOL 270MHz spectrometers are presented with a form to complete on setting up a spectrum: the default file names are not very helpful. Many users have taken to creating very long file names, but this creates problems - see below. The GSX user fred actually gets their NMR spectra put in directory /usr/people/fred/files/data by default. (If they convert files to a different format they should go to /usr/people/fred/files/foreigndata) This only matters to users if they try to copy files directly from the spectrometer workstations. Long file names will work on the Unix-based workstations of the 270s but will be unhelpfully truncated by the recommended PC software - some files will not even copy correctly to other discs (or from copies back into the 270's computer! ) I strongly recommend that you try to use a maximum of 8 characters as a file name - enough for initials and a sequence number. If you use the Auto feature of the Delta software you should limit the name to 5 characters if possible.
I frequently see file names which are unintelligible to the PC software. The unmemorable name of this Unix-based server was assigned by the network administrators. This computer should be accessible to Windows machines via “Network Neighbourhood” or its equivalent.
Opening the computer icon should show a variety of more or less self-explanatory directory names containing data from spectrometers, notes, and bits of software. All our spectrometers are able to transfer data to PC-format floppies and/or 100Mb Zip discs, but it will probably be MUCH more convenient to read data from the NMR file server - at this moment the GSX-270, the 300MHz and the 400MHz are on line, and most recent service work run on the 500MHz gets transferred to the server. NMR data can be copied to your local PC disc or used over the network. Remember that the 300 and 400MHz produce data sets which are files in directories - these must be copied intact. This is described in more detail in the notes on MestRe-C.
Users of the EX-270 will find notes on transferring its data to floppies in the docu directory of Chnmr3: there is no immediate prospect of a network connection to this spectrometer. Regular users will find it more useful to map the required section(s) of the server data to drive letters.see the appropriate Windows help files. Software exists for Apple systems to read the network “shares” provided by the server but I have not tested it in the absence of useful NMR software. Desktop Data Processing for NMR on PC systems. Our modern systems store both the initial FID and the phased and (hopefully) correctly calibrated spectrum - most users will probably use the stored spectrum. Our older systems normally give one or the other, which means that users will be obliged to retransform and phase the data in many cases. These operations should be straightforward for spectrometer users, but there is one important point which seems to be poorly understood - probably because spectrometers tend to automate and hide it.
When an FT spectrometer is used to record a wide shift range (in practice, anything other than standard proton spectra) the interval between the data points along the shift axis is likely to be wider than at least some of the lines of the spectra. In these circumstances, if a simple Fourier transform is applied to the FID, there may be only 1 or even no data points on these lines in the calculated spectrum - at best, lines may have wrong intensities, at worst they can be lost.
To avoid this unacceptable result, it is conventional to multiply the FID by a decaying exponential function before the transformation. This causes all lines to have a well defined minimum linewidth, chosen to give acceptable spectra. Various computer programs call this process exponential multiplication, apodization, applying a window function, etc. In some cases an adjustable exponent is displayed with the FID, in which case the exponential curve should be adjusted to be near zero at the right hand side. In other cases a line broadening factor must be entered - try 2 or 3 to start with. (This is the width an infinitely narrow line would convert to.) This process not only broadens lines to ensure they are properly recorded, it removes much of the noise from the latter part of the FID, improving signal/noise ratio. In noisy spectra the broadening can be adjusted to trade off line width against noise.
The essential point to be made is that when a FID file from any non-proton spectrum is to be Fourier transformed, you MUST use the relevant section of your PC software to apply an exponential multiplication before the transform. Failure to do this will produce VERY inferior results.
MestRe-C, a free program for NMR data processing on PCs, has been produced by a group at the University of Santiago de Compostela, Spain. This program is recommended for use as it works well, has built-in help files, and can cope with data from all our spectrometers. The program can be obtained from Department file servers or downloaded from the web as a compressed archive. I keep an older version (mestrec23) on Chnmr3 - this only works for 1D spectra but is relatively small, runs on older versions of Windows, and has well-written help functions.
It may be more suitable for some users than the newer versions (currently 3.5.n), which require WindowsXP/2000. The new version is much more ambitious and handles 2D data efficiently, but the help function seems very unfinished as yet. The program's help menu points to the web site of the group who produce it: their site also advertises other NMR packages - see the final paragraph of this note.
If you use the file server, you can either copy data to your computer or use MestRe-C to directly open the files over the network by working through to the required file in the file open window. Users of software such as MestRe-C cannot avoid some of the complications of NMR file formats, which are completely unstandardised. (Regular attempts have been made to promote a standardised format (JCAMP) but there is no commercial benefit in adopting it.) Files are opened in MestRe-C version 2.3 via the open option in the file menu which allows you to select an appropriate file type first.
In newer version files must be read in via the Import Spectra option, but the correct file format is normally chosen automatically. Data from our spectrometers must be processed as outlined in the following sections. Modern Bruker systems - 300 and 400MHz. These hold data in data sets, with names like J1234 or Jun14: each data set can contain 1 to 999 experiments. The data set name is a directory (folder) containing sub-directories named 1, 10, 400 etc., - Bruker refer to these numbers as EXPNOs. The data set name and EXPNO are listed at the top of peak listings. The EXPNO sub-directories contain a standardised set of files which must all be present.
If a data set contains only the data you want, the whole thing can just be copied in the usual way. If you need to copy part of a large set, make a new folder (directory) on the disc you are copying to, give it the same name as the data set, and copy over the sub-directories with the required EXPNOs. Do not make any changes to the files inside the EXPNO directories! MestRe-C can open these files by selecting the file type Bruker UXNMR/XWINNMR (in version 2.3): then work down through the data set name and the EXPNO to a list of files which includes one called fid.
Double-clicking this would open the FID: alternatively open the folder pdata, another folder usually labelled 1, and reach a set of files including 1r. Double-clicking this opens the spectrum. Users will in many cases find it more convenient to use the package supplied by JEOL The Delta program which runs these spectrometers saves data in its own format which MestRe-C (Version 2.3) cannot read directly. The latest (3.5 or higher) versions of MestRe-C can handle files in Delta format but they may cause problems if not copied first to the local disc. FID files transform correctly: files containing spectra get the wrong shift scale (correctable but unhelpful). In all cases the chemical shift calibration is lost.
The spectrometer's own software can however convert stored data to an older JEOL format which can be handled by all versions of MestRe-C - but this must be done at the spectrometer. Whichever package is used, problems will be caused by long file names: like many PC packages, MestRe-C and SpecNMR truncate long file names to 8 characters with results which can be fairly unintelligible. (Many users have got into the habit of using long file names on these spectrometers, but these can cause various problems. Some of these files refuse to copy to Zip discs: some more give problems if the files are transferred to CD-R discs. If the CD-R is read on most non-Windows systems including the 270's own SGI workstation, ALL the file names are truncated to 8 characters.) The file conversion procedure using the spectrometer software is as follows: at the same time I strongly recommend you give the data a new name of 8 characters maximum, using only A-Z and 0-9. In the Delta window (the first one to appear when the software starts up) select File Conversion in the File menu - a new window appears.
This has text fields for FROM file and TO file, and 2 columns of buttons headed FROM file and TO file. In the FROM file column, click Delta: in the TO file column, click JEOL:GSX/GX/EX. Click the FROM file button next to the text window. The usual file selection window will appear - choose the required file as usual and click OK. Click the TO file button next to the text window - a similar file selection window appears, with buttons dimmed.
Type the new 8-character (maximum) file name in the text box at the bottom of this window, ending with the return key. The buttons become active - press OK. Click Start - messages appear in the box at the bottom of the window. Click the Close button when finished. Each conversion will have put 2 files into the files/foreigndata directory, named filename.gxd and filename.gxp.
BOTH of these files are required and should be copied over to your own system. Once they are successfully copied, you must delete them from the workstation disk - there is never enough space! In MestRe-C, select the file type JEOL (version 2.3) and open the filename.gxd file - remember that the other file (filename.gxp) must be present. Old Bruker systems - 250 and 500MHz. These have very non-standard old computers: data can only be extracted via a slow link to a PC running a genuine DOS system.
(2 or 3 spectra a minute if nothing goes wrong.) Files have names of the format ABCD.123. The transfer program has various options: the data should be stored as 'Aspect Format' files and will have the same filenames. MestRe-C can open these directly: select the file type Bruker Aspect 2000/3000 for version 2.3. Bruker WIN-NMR FILES. Some of you will have files converted to the format used by Bruker's WinNMR program.
(This is an expensive PC-based package with many similarities to MestRe-C - at present it is running in the PCs attached to the 300MHz and the 250MHz.) An old-style Bruker file named FRED.123 will have been converted to a directory named FRED containing a set of files named 123001 with various suffixes. A file which was originally EXPNO 20 of data set Jun14 will be a directory named Jun14 containing files named 020001.suffix. In MestRe-C, select the file type Bruker WinNMR, work down to the numbered files, and double-click the file with the suffix 1r to open the spectrum (or the suffix fid for the FID).
Software on MestRe-C web site. The MestRe-C web site also offers a variety of other PC programs related to NMR. There is also a link to a site offering an NMR program (“SwaN-MR”) for Apple systems. I spent a long time testing this, as it looked potentially useful to the Department. However, it is very much the work of one enthusiast, who assumes users will always want to retransform the data, rephase the spectrum, and so on. It is possible to get it to read some spectra directly, but it then seems impossible to set correct shift scales.
Printing and pasting data into documents seemed poor on my G3 machine. The package includes a weird help utility, which lacks such luxuries as an index, and various bits of the software seem not to work as advertised. I honestly do not feel it will meet the needs of most users. MestRe-C can be run on modern Apple systems by using a PC emulator - I have VirtualPC running Windows98 - this costs a significant amount but works well. MestRe-C can export data as Windows metafiles.
Attempting to cut and paste spectra between PC and Apple environments is not satisfactory. JEOL have provided this software on a Departmental site licence: the software and various help files may be found on the server Chnmr3. The present version will process 1 dimensional data from both 270MHz spectrometers. The software is best used to read FID files - these are the default files saved by the Delta software. (In the file open window make sure the correct file type is selected - usually JEOL delta.) The software does fail to correctly read shift calibration. Resetting this is usually simple for GSX data, but EX users may need to know either the mid-point of the original spectrum or the position of a line in the spectrum.
More details of short cuts to do this are in the help files on Chnmr3. The current versions (3.4+) of MestRe-C can read the transformed 2D spectra stored by the NMR service spectrometers, which most users will find the most convenient way of working with and replotting these spectra. There is an extensive help file (pdf document) which rather assumes familiarity with NMR jargon. The same group also produced a 2D-only package (MestrecND) for older Windows version which I no longer recommend - it was necessary to retransform the raw data, which required some understanding of relevant window functions and zero filling. Wrong choices could produce very poor results. To display 2D spectra with the current versions of MestRe-C, from import spectra select a dataset, an EXPNO, pdata, usually the directory '1', and double-click the file rr. You may need to press + or - a few times to get a sensible display.
It is possible to control the exact size of the plot (COSY is conventionally plotted as a square) and to add related 1D spectra along the axes. Processing 2D data in MestRe-C MestRe-C will process 2D data but some background knowledge is essential - I assume that very few users will want or need to do this. In all these techniques, a series of multipulse experiments collects a sequence of 1D spectra. The information which will provide the second dimension is stored in these individual spectra as systematic variations of the phases of the various signals.
Delta Software For Nmr Database Download
The individual transformed spectra are stored in the rows of a matrix and a further transformation applied to the columns produces the required 2D spectrum. Collecting the large number of spectra requires a significant time, and considerable memory is required for manipulation and storage. It is therefore usual to collect the minimum possible amount of data and to “zero fill” the data matrix before the final transformation: this does degrade the shapes of the peaks in the second dimension. (Very) basic processing of 400MHz COSY and 1H/13C correlation spectra. Open the data set to find the file ser. The screen fills with a pattern representing the untransformed data. In the process menu, select Fourier transform to get a dialog box.
This box will show the correct size of the FIDs in the data (leave alone). Click the apodise box to get a tick and click choose function. Select SineBell and leave the factor at zero.
The other choices in the FT dialog should be left at their defaults: click apply. The display changes to vertical stripes (or blank) and the FT dialog appears again.
The size setting should normally be changed to 4 times its initial value (zero filling). Set apodize and choose the function as before and apply the transform. The result should be a 2D display but it may be rather empty until you click + in the toolbar a few times. Many of the useful controls are in the view menu, such as turning contours on or off. Shift calibration in each dimension may need to be checked by marking a known peak - see tools menu. Proton COSY spectra usually look better if symmetrised (Process menu) and forced to be square.
Read the help file supplied with the package! There is much excellent expensive software available for PC systems: some of you will be familiar with Bruker’s WinNMR. This is in use in the Department, but is both expensive and apparently being phased out by Bruker - it will not be updated by Bruker to keep up with changes in Windows systems. At present, it is possible to obtain a free WindowsXP/2000 version of the Delta software which runs the 270MHz systems for desktop use.
Although there is no charge, the software needs to be downloaded from JEOL's site in the USA (www.jeol.com and look for NMR and delta software.) and must be registered via e-mail to the machine it runs on, which is somewhat tedious. (The software is essentially tied to the PC's network card.) This is not quite the same as the software in the spectrometers but should present no real problems to experienced users. The software will plot perfectly well but spectra cannot easily be exported into other files such as word processing documents. This is supposed to improve in newer versions. The software also has the annoying quirk of only working on data which has been copied to the PC's local disc.
It will nominally read files in other formats but reading modern Bruker files is particularly clumsy and not very useful to us. There are other free packages, but all the ones I have tried are less suitable for our purposes than those described above - they either require data file converters (not always free) or cannot cope with more modern spectrometers such as our 300 and 400MHz systems. Apple users are poorly served with NMR software. I have found nothing free that I could recommend to ordinary users.
Delta Software For Nmr Database Windows 10
There is a commercial package which has UK users - I got a thirty day trial version and took an instant dislike to it because of the very clumsy user interface. A working version is moderately expensive. My own solution was to buy a version of VirtualPC for my G3 - this accesses Chnmr3 correctly and runs software such as MestRe-C 2.3 and SpecNMR correctly. HSR has documented a method of logging in to a remote PC from an Apple system and running the NMR software: I believe this requires Apple OS 10, but I have not tested it.
Users of the 250, 270, and 300MHz spectrometers are responsible for making backups of their own data on these systems. NMR staff will arbitrarily delete old data files if these systems run out of disc space - you have been warned!
In the past, the use of 100Mb Zip discs for backup has been suggested, but changes in the marketplace are making this advice obsolete. It is no longer possible to get some types of Zip drive unit replaced if (when!) they fail, the discs themselves have remained expensive, and CD-R discs and drives have become much cheaper. Some users have suffered total failures of individual discs.
I therefore recommend that users should use CD-R (not CD-RW) discs and make sure that they write discs in a format which can be read by the CD drives of most computers. Given the low price of blank discs (especially in comparison with Zip discs) there is no great compulsion to use all of the space on a disc! I usually produce discs in ISO9660 format with the Joliot modification to allow long file names. (This is usually the default format for data discs in PC software.) My experience is that it is better to copy the NMR data to the local disc of the PC making the CD-R rather than trying to copy files from the server over the network to the CD-R The NMR service has several years of 400MHz data on CD-R: over a year's 500MHz data is accessible via the server.
The Department has 6 general use systems for solution work - RVL has additional systems for solid state work The NMR service uses 400MHz - a Bruker 2 channel DRX-400 spectrometer with a pulsed gradient system for 2D work and a sample changer. 500MHz - a Bruker AM-500 spectrometer.
This very old spectrometer is still acceptably reliable but its features and performance reflect its age. Open access spectrometers 300MHz - a Bruker DRX-300 spectrometer used for proton and carbon-13 work, running Bruker’s IconNMR software.
270MHz - a JEOL GSX-270 spectrometer updated with the Delta software and hardware package. This system has facilities for proton and carbon-13 and is fitted with a 16-place sample changer. 270MHz - a JEOL EX-270 spectrometer updated with the Delta software and hardware package. This is a multinuclear system.
250MHz - a Bruker AC-250 spectrometer. This system has a quad-nucleus probe (1H, 19F, 31P, and 13C) R.N.S.
Delta™ is the software that empowers our ECZ, ECS, ECA, and ECX series NMR systems. Never has a software package with such powerful control and processing been so easy to use. Multi-dimensional visualization (up to 4D) and processing (up to 8D) are just part of the standard package. Standard Features New!. Object-oriented, multi-dimensional data manipulation. Digital filtering.
Fourier transform. Multi-dimensional phasing. Notch and high-pass filter. Linear prediction, BLIP and FLIP. Baseline correction.
Deconvolution. Automatic peak detection.
Data presentation and plotting. Data format import and export utilities Delta™ runs on the major platforms: WINDOWS™ and Mac OSX.