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
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
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
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
spectrometers run the network service "samba" to export network shared
drives in a Windows-compatible format.
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:
(400 in Malott)
(400 in SBC)
(cryo 500 in Malott)
(open access 500 in Malott)
(CMLD 400 in SBC)
(800 in SBC)
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
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.