Accessing SYBYL through an Xterminal

About SYBYL

Sybyl is a molecular modeling program from Tripos Associates. It can be accessed over the network as an X11 application by an Xterminal or any Macintosh running an X server application like MacX or a PC running Xone.

Of course, you can't get the nice graphical output one can get by viewing it on an SGI, but all the manipulations can be done (e.g. energy minimization).

Overview

Sybyl runs on an SGI. It can be accessed by one of the Xterminals in the Molecular Modeling Lab (room B50c) by telneting to mmlab (an SGI 2 processor Challenge L server).

You must have a CMGM account through a Bioinformatics Resource membership and an account on mmlab.

Operation

• Log on to one of the Xterminals in B50c (Beckman Center).

  Log into pmgm.stanford.edu and use your cmgm account and password

• Use the right mouse button (any where on the blue desktop) and bring down the WORKSPACE menu.

• Choose the SYBYL MMLAB Login option

• At the mmlab prompt, type sybyl

Trouble Shooting

• No output to the screen.

  If you get the message "can't open display", then you will have to set the DISPLAY environment variable. This is done by typing:

  setenv DISPLAY machinename:0.0

  Of course, substitute the name of the computer that you are sitting at in place of machinename.

• Sybyl won't exit when you use the pull down menu.

  Sybyl will prompt you for a "yes" answer to really quit if you have done any modifications to a molecule. The window that prompts you is often buried behind the molecule display. Use the key on the keyboard marked "front" to pop up the window that is waiting for input.