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Radboud University Nijmegen
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Accessing the CMBI Cheminformatics Services on the Internet

Many Cheminformatics services provided by the CMBI use programs (applications) that require interactive graphics (e.g., for sketching structural formulae). Which of these applications can be used on a remote computer terminal depends on the capabilities of the local computer and on the way in which a user connects to the CMBI host computer system (cheminf.cmbi.ru.nl):

The table summarizes the (graphics) functionality of the various types of access, the software needed on the desktop machine, and the applications that are available through that access mode.

Type of access Required software Sample applications
No graphics terminal emulator MOPAC, Babel
X-Windows graphics X server or emulator CSD, Sybyl, LHASA
Client-server client software CrossFire, ISIS
WWW application web browser ICSD

However, terminal and X-Windows access needs to be secure nowadays.

 

Secure shell and secure FTP access

If you wish log on to cheminf.cmbi.ru.nl for interactive usage (e.g., MOPAC, CSD) you need to connect to cheminf.cmbi.ru.nl using secure shell (ssh). Note that is not an issue with the WWW and client-server applications mentioned above.

Windows

For Windows PCs there is a free secure shell client called Putty which you can download and install. On the same download site you will find a secure FTP client (psftp) and a secure copy client (pscp). You can use either one of these clients if you wish to copy files between your local machine and cheminf.cmbi.ru.nl; an alternative is WinSCP.

Example use of pscp to copy files from your local machine to cheminf.cmbi.ru.nl (from an MS-DOS window), assuming your account name on cheminf.cmbi.ru.nl is userid and you wish your file(s) to be copied to directory pathname on cheminf:

pscp.exe *.rpm userid@cheminf.cmbi.ru.nl:/pathname

You will be asked for the corresponding password on cheminf.cmbi.ru.nl, and then all files with the extension rpm in the current directory of your local machine will be copied to the directory /pathname on cheminf.cmbi.ru.nl. Of course userid must have permission to write into this directory.

Unix/Linux

If your local machine uses Linux for an operating system, ssh is usually available, either directly (as normal part of the operating system) or from the installation disks. For all other Unix systems, if ssh if not present you can use the secure shell client openssh available from http://www.openssh.com/.

Example of logging on to cheminf.cmbi.ru.nl (assuming your account name on cheminf.cmbi.ru.nl is userid):

ssh -l userid cheminf.cmbi.ru.nl

or:

ssh userid@cheminf.cmbi.ru.nl

or (for the -X flag, see next section):

ssh -X -l userid cheminf.cmbi.ru.nl

If you have problems with installing or running secure shell, you are advised to consult your local system manager first.

To copy files between your local machine and cheminf.cmbi.ru.nl, you can use sftp (secure ftp) which should be available in the same way as ssh.

 

X-Windows (X11) access

A number of applications (e.g. CSD) require X11 graphics, also called X-Windows graphics. X-Windows requires an X server on the local computer and a fast network connection. Unix machines almost always have X-Windows capabilities, but for Macintoshes and Windows PCs additional software (an X server application, also called X emulator) must be bought and installed.

Windows

Several commercial X emulators are available. Two of the X-Windows emulators that can be used with the Cheminformatics services are XWin32 and Exceed. You are advised to check first with your local computer department/system administrator whether your site has already licensed an X-Windows emulator.

X applications on a remote host (e.g. CSD on cheminf.cmbi.ru.nl) require accessing your screen, and the remote host must be given explicit permission to do so. This permission is given from within the X emulator program. The following instructions are for Xwin32; for other emulators you will have to consult the manual to look up the required functionality. To give the remote host (cheminf.cmbi.ru.nl) permission to access your local screen, you must add cheminf.cmbi.ru.nl to the XHost list in the XUtils menu. Note that in newer versions of XWin32, XUtils has been replaced by XConfig which has a Security panel where you add the host name cheminf.cmbi.ru.nl and then check the Access control option.

Since X-Windows is considered to be an insecure protocol, users will have to use X-Windows tunneling via the secure shell client mentioned in the previous section. In Putty, that is called enable X11 forwarding. You do that by checking the X11 forwarding box in the Tunnels panel (note that newer versions contain a separate X11 panel).

Important:
When using X-Windows tunneling/forwarding, the DISPLAY variable should no longer be set by the user (that was pre-ssh usage).

To establish an X-Windows-enabled session, you first call the emulator server program and then start up an ssh session. Note that you do not start up an X-Windows session, the emulator runs just in "listening" mode. You can check the proper working of X-Windows by issuing (after logging on to cheminf.cmbi.ru.nl) the xclock command. A window should pop up to ask you whether you allow the access to your screen. If you don't want that question popping up all the time (probably you don't!) you can check the appropriate box.

Unix/Linux

Unix/Linux machines should already have an X server as normal part of the operating system and using X applications should then be straightforward.

X applications on a remote host (e.g. CSD on cheminf.cmbi.ru.nl) require accessing your screen, and the remote host must be given explicit permission to do so. This permission is given by typing the command (on the local Unix machine!):

xhost +cheminf.cmbi.ru.nl

Users that run a secure shell client under Unix/Linux need just to supply the -X commandline flag, e.g. (assuming your account name on cheminf.cmbi.ru.nl is userid):

ssh -X userid@cheminf.cmbi.ru.nl

Important:
When using X-Windows tunneling/forwarding, the DISPLAY variable should no longer be set by the user (that was pre-ssh usage).

After logging on to cheminf.cmbi.ru.nl, you can check the proper working of X-Windows by type in the xclock (or xclock &) command at the Unix command prompt.

XMenu

The File Manager (XMenu) program is a versatile file and session manager. It is also a useful tool to access the Cheminformatics programs. As the name indicates, it is an X-Windows application. You can call XMenu by typing xmenu (or xmenu &) at the Unix command prompt.

Alternatively, and possibly preferred by more experienced (Unix) users, you can type in commands at the Unix command prompt directly to start up the programs you need. You can append a "&" (ampersand character; see above xmenu example) to any command to start it up in a separate command shell and keep the original shell available for other commands. Note, however, that you cannot use an ampersand with the Sybyl command!