How to retrieve your EM data

How to download your data from NYSBC

• You should already be set up with an sftp account to sftp.nysbc.net
  

password

sftp> cd /mnt/cemdata sftp> ls jeol_1230 jeol_2100 jeol_3200 tecnai

• You will see a list of microscope directories: j1230 ; j2100 ; j2100 ; tecnai
• Change to the appropriate microscope, then to your directory

     sftp> cd tecnai/<your username>
     sftp> ls
     temdata
     sftp> cd temdata
     sftp> ls
     [... list of files and directories]
    sftp>  get myimage.dat
  

   sftp> bye

Hints

• Don't put any spaces in filenames or directory names
• If you absolutely insist on putting spaces in file/directory names, need to enclose them with ' ' when using sftp.

   sftp get 'my filename that has spaces.mrc'

• Can use * and ? to get multiple files
  • * matches any number of characters
  • ? matches any single character
  • example: image*.mrc will match image.mrc, image001.mrc, image_bunchofstuff.mrc
  • image???.mrc will match image001.mrc, but not image.mrc, image01.mrc
• For obvious reasons, don't put * or ? in your file or directory names

• If you are unable to log in to the sftp server, contact rice@nysbc.org

GUI for transfer

Client Software

1. SSH Secure Shell for Workstations - Compatible client with both Windows and Unix is available at -
   http://www.ssh.com/support/downloads/secureshellwks/non-commercial.html. Unix versions may require complilation.
2. GFTP - GFTP is a compatible client for Linux systems available on Linux 7.2 and higher. It can be downloaded from
   http://gftp.org. To access the NYSBC SFTP Server Version 2.0.9 or higher is needed.

Connecting To The SFTP Server

• Using Windows GUI with SSH shell Type in Host Name and your User Name. Leave all other settings the same, as shown in figure 1

Figure 1

• Enter Password at password screen

Figure 2

• Change to the /mnt/cemdata/ directory to view a list of microscopes.

Figure 3

• Change to your appropriate directory and transfer files using drag and drop or select, right click, and download.
• Using SFTP2
  1. Type sftp2<username>@sftp.nysbc.net into a terminal window, enter password when prompted.
  2. Change directory to /nysbc_nmr.
  3. Spectrometers are listed in the /nysbc_nmr directory.

SFTP2 allows use of the following commands -

• Set ALLOWTOPICVIEW =

-- BillRice - 02 May 2008