Quick start with ACD 1D/2D NMR Processor, Version 11


The software only runs in a Windows environment (this is ACD's choice), though we have been told it will run on the newest Mac with Intel processors.

In order to install the software and check out a license to use it, you must be connected to the chemistry/pharmacy Novell server tree and be able to see the network share called "Apps" on your computer.  If you don't have this access, see your designated computer support contact (the NMR Lab cannot make or troubleshoot these connections).

Inside the Apps folder, go to PC_APPS -> Scientific Tools -> ACD_LABS_Software_10_0.  Inside this folder is a text file called "lic" that contains all of the license information for our site--open the file with Notepad or WordPad and just copy and paste into the boxes as you are prompted to do so.  To start the installation, open the folder called install and then double click on the install icon.  After you supply the license information, copying the files to your computer will take several minutes.  You will have the option to check for and download any program updates from ACD during the process.  At the end, you will have a new ACD LABS 10.0 tab under the All Programs menu in Windows.  From there, you can start either the 1D or 2D NMR Processor programs, or various helper applications.

In order to work with Bruker data, copy the data folders from the spectrometer or workstations onto USB stick, CD, floppy, etc. and get them on your computer.  Inside the ACD program, you can choose to open an existing file immediately, or do File -> Open -> From 1D NMR Directory and then navigate to the raw data file.  For a typical 1D Bruker spectrum, there is the main data folder, one or more numbered data folders inside that, and inside the numbered folder, a file called fid (1D data) or ser (2D data).  Click on this file and a small image of the raw data should be displayed.  Then click Open, which will display the raw data in the main window and open many new context sensitive drop down menus and icons.  With raw data, buttons for apodization and fourier transformation will be displayed.  The defaults imported with the data are normally OK.  After an FT, buttons for phasing, peak picking, integration, multiplet definition, and assignment are displayed.  There are also ChemSketch and Processor tabs at the bottom of the screen for rapid switching between those two modes.  In ChemSketch, you can quickly draw a 2D sketch of the structure and then tag signals in the spectrum with protons or carbons in the sketch. 

Many functions have an "auto" button that you can try without having to understand all of the options at the beginning. There is also extensive help available on a list of alphabetized topics which you can see under the Help menu.


Quick start with MestReNova NMR processing software

This software will run under Windows, Mac OS X, and various versions of Linux (with installers specific to the Linux release).   You can download the appropriate version for your computer from 
http://www.mestrec.com/descargas.php?idp=1&i18n=1
Choose the highest numbered (most recent) release version and save the downloaded file to your computer.  This is a self extracting installation program.  Download the manual at the same time!
You will need a license file, which Dave or Sarah will email you on request.  Save this license file to your computer also.  We have a permanent 150 seat license for the NMR processing features; also, we have a demo license for the chemical shift prediction module through July 2008.  You do not need to download any additional software to try this out, but you do need to have a separate license file for chemical shift prediction.
After you run the installer and start MestReNova, you will be prompted for the location of the license file.  Browse to its location (your desktop, for example), and click OK.  You will need to exit and restart MestReNova for the license to work.
Opening a Bruker data file in MestReNova is similar to the ACD software, except in most cases you will not need to do any explicit processing of the spectrum--the processing parameters used in TopSpin will be copied and applied automatically.  This works for both 1D and 2D spectra.  Opening multiple spectra will start a PowerPoint-like column of thumbnail images of the spectra you have open.  As with PowerPoint, if you save this file, you save all the slides.  You can export directly to PDF format and choose to save one, multiple, or all spectra open in MestReNova to the PDF file. 

Retrieving data under Windows from the NMR spectrometers and the server

        Our NMR spectrometers run the network service "samba" to export network shared drives in a Windows-compatible format.
    To use it as a network drive under Windows, go to My Computer -> Tools (or My Network Places -> Tools in Windows 2000) and choose Map Network Drive.  Choose an unused drive letter.  In the Folder box, put the name of the spectrometer you wish to connect with, or the server:

\\florence.msg.ku.edu\topspin            (400 in Malott)
\\yosemite.msg.ku.edu\topspin           (400 in SBC)
\\siena.msg.ku.edu\topspin                 (cryo 500 in Malott)
\\paris.msg.ku.edu\topspin                 (open access 500 in Malott)
\\bigsur.msg.ku.edu\topspin               (CMLD 400 in SBC)
\\grandteton.msg.ku.edu\topspin        (800 in SBC)
\\kunmr6.msg.ku.edu\home\user        (600 in MRB)
\\kunmr-suse.msg.ku.edu\data1         (server)

and then click Connect using a different user name.  Enter the user name nobody and the password (ask the NMR lab staff if you do not know) and click OK.  Click Finish in the Map Network Drive box; in a few seconds, you should get a new directory view window of the topspin tree.  As usual, go down the tree data -> your username -> nmr to get to the data folders.  If you had samples run on the 800, the data is probably in the nmrsu/nmr folder.
    To do the same operation on a Mac, choose Go -> Connect to server.  In the box that appears, type smb:// followed by a machine name as shown above.  Note the forward slashes here, back slashes for Windows.  At the next step, you will be prompted for the name and password (same as above).
 
        Everyone has read permission to the data in all the trees (this is exactly the same as on the spectrometer).  Read permission also gives you permission to copy to anyplace you have write permission (such as the desktop of your own computer or Novell network drives you may have).  The nobody account does not have any write access. (Write access in Linux also grants permission to delete files.) 

      The server has all of the archived data available, stretching back in some cases to 1997.  The data1 folder contains a folder for each instrument which mirrors the layout of its data, and you proceed down the directory tree to get it.  Non-data files (for instance, contents of your home directory with the exception of directories ending in .fid on the Inova 600) are not backed up. The server is updated each night from the spectrometers, which means that the current day's data will not be visible on the server.  However, old data that has been removed from the spectrometers should still be available there. There are permanent network drives on the Linux workstations in 3002 Malott and 104 SBC.  The path is /opt/server and subdirectories take you to archived copies of data from each of the spectrometers.

       From off campus, you can access the network drives, and get a license to run the ACD software, if you  set up and run the "KU Anywhere" VPN software on your computer.  It is accessed through the Kyou portal. Log in to Kyou and you will see the link KU Anywhere in the upper right side of the page next to Welcome, (your name). If you click on this link, your computer will go through a security check, download and start a Java applet, and you will have a secure tunnel to the KU network and a KU network address.  This allows you to do most of the things you do on the KU network.  Note that this is a KU-wide network service and the NMR lab does not make or troubleshoot these connections.

Dave 06/16/08