User Guide for Data Transfer

(From AVIII 400 to NMR Server)  

November 11, 2012

The CBC NMR Laboratory

University of Delaware

ii

 

1   Introduction  ...........................................................................................................  5  

2   NMR  Data  Transfer  .................................................................................................  6  

NMR Data Transfer

iii

List of Figures

Figure 1: The Blue Folder ................................................................................................................ 6  Figure 2: Terminal Command Shell ................................................................................................. 7  Figure 3: gFTP Interface – 1 ........................................................................................................... 8  Figure 4: gFTP Interface – 2 ........................................................................................................... 9  Figure 5: gFTP Interface – 3 ......................................................................................................... 10  

NMR Data Transfer

4

PREFACE

Purpose of This Document This user guide aims to help you to transfer NMR data collected on AVIII 400 NMR spectrometer (located in 049 BRL) to the NMR server.

Intended Audience This document is intended for users of the AV400, AVIII 400, and AV III 600 spectrometer. It is assumed that user account has been created for the user on these instruments.

NMR Data Transfer

5

The NMR workstations in 045 BRL are mounted to the NMR server through network. After the NMR data are collected on the AVIII 400 MHz NMR spectrometer, it is highly recommended to transfer the NMR data to the NMR server as a key stage of data backup. After the data are transferred, the workstations in 045 BRL can be used to access the NMR data collected on AVIII 400 NMR spectrometer. Use the workstations in 045 BRL can be used to transfer the NMR data.

The NMR workstations are preloaded with Bruker TopSpin software and other NMR data processing software.

Login information, including login name and password, will be provided by the NMR spectroscopist after the NMR training on the AVIII NMR 400 MHz has been completed.

NMR Data Transfer

6

Follow these steps to transfer NMR data from the AVIII 400 NMR spectrometer computer to the NMR server.

1. Before transfering the NMR data from AVIII 400 MHz NMR spectrometer to the NMR server, make sure the workstations have been set up according to the procedures described in the “User Guide for Setting Up NMR Workstations”

2. In the desktop of the NMR workstation, click on “blue folder” as shown in Figure 1 and select Terminal from the manu, a new terminal shell window appears as shown in Figure 2.

Figure 1: The Blue Folder

click  on  this  blue  folder

NMR Data Transfer

7

Figure 2: Terminal Command Shell

3. In Terminal command shell, after propmt sign $, type mkdir to create a directory for the data to be transferred. In this example, a directory called drx400 is created. Other directory names, such as AVIII, can be used. Type cd drx400 to change directory to the drx400. After getting into the directory of drx400, create a directory called data by typing mkdir data. Then get into the directory data by typing cd data. At this level, create a new directory which is named after your username. To do so, type mkdir ccui, where ccui is a username. You should replace “ccui” with your own username. Get into the directory of ccui by typing cd ccui and then create a directory call nmr by typing mkdir nmr. Finally get into the directory nmr (cd nmr) and type pwd to show the current directory. Now a path /home/xdata/ccui/drx400/data/ccui/nmr and the assoicated directories are created for incoming data.

Note: the directory ccui is used as an example here. It should be replaced by your own username.

4. Click on the “blue folder” again and this time select gFTP from the manu. A gFTP window appears as shown in Figure 3. In the field of host, enter the computer IP address (128.175.138.54) for the AVIII 400 NMR. Click on the field of User, fill in your username on the AVIII 400 spectrometer. Finally click on the field of Pass and enter your password of the AVIII 400 NMR.

make  sure  “ccui”  is  replaced  by  your  own  user  

name

NMR Data Transfer

8

Figure 3: gFTP Interface – 1

5. When entering login information the first time, you will be prompted by gFTP interface to confirm a security inquiry. Just enter “yes” as indicated in Figure 4. A similar procedure is followed for the password. The password may be required for twice.

enter  your  user  name

NMR Data Transfer

9

Figure 4: gFTP Interface – 2

6. Once the network connection is established and the user authenticity is verified, gFTP interface (shown in Figure 5) provides two data panels: the left panel is for the NMR server and the right panel is for the AVIII 400 NMR workstation. On the left panel, type in the directory path as /home/xdata/ccui/drx400/data/ccui/nmr.

On the right panel, enter the NMR data path on the AVIII 400 NMR spectrometer computer, for example: /opt/data/ccui/nmr.

enter  “yes”  here.

NMR Data Transfer

10

Figure 5: gFTP Interface – 3

7. To transfer a data folder from AVIII 400 NMR computer to the NMR server first click on the folder to be transferred in the right panel of gFTP interface, then clcik on a transfer triangle as shown in Figure 5. The transferred NMR data folder is then appeared in the left panel. The details of data transfering are shown in the gFTP message board. As a step-by-step example (Figure 5), a data folder “test” is being transferred from the AVIII 400 NMR computer to the NMR server.

a.  click  and  highlight  “test”

b.  Click  this  icon  to  start  data  transferring

c.  “test”  is  shown  here  after  transferring  is  

finished

NMR Data Transfer

11

8. After the data transfer, first starts the TopSpin NMR software, then righ-click on the left panel (the data broswer panel) of the TopSpin interface, select “Add New Data Dir…”. Type in the data directory path as /home/xdata/ccui/drx400 when propmted, an NMR data directory is then shown in the data borswer panel, from which the transferred data can be accessed directly by the workstations in 045 BRL.

Remember  change  “ccui”  to