SYBYL is the major molecular modeling software at MUSC. It may be accessed from any UNIX workstation or remotely as long as the remote PC or MAC have X-server software.
A new computer is now hosting the SYBYL software here at MUSC.
The new server is named:
erg3.musc.edu
This machine is an IBM xSeries 336 with 2, 3.8GHz CPUs and 8 GB of memory. This server is attached to an IBM DS300 disk array with a usable capacity of 1.5 TB.
SYBYL requires that you have some X-terminal capabilty on your desktop or laptop computer.
If you have a MAC with OSX or LINUX or a WINDOWS machine with X-terminal software (for MAC OSX users, you probably have to instal Xterm from the distribution disc) you can easily run SYBYL. Simply open an X-terminal text window and type
xhost +erg3.musc.edu
This tells the your machine to allow windows from erg3 to appear on your machine.
SYBYL users can use SecureShell to connect to erg3 via a command line such as :
ssh -X username@erg3.musc.edu
After the prompt for erg3 appears, type 'who' and note the identity of your computer on erg3. If you do not know the IP number of your computer see
setenv DISPLAY reggiesmac.bsb.musc.edu:0
or
setenv DISPLAY 128.23.103.111:0
Obviously reggiesmac and 128.23.103.111 will need to be replaced by names/numbers specific to your PC.
At a user prompt type one of the following:
ssh -X username@erg3.musc.edu
OR
ssh -Y username@erg3.musc.edu IF you are using a G5 MAC with OS 10.4+
The -X and -Y set up the xhosts and tell the remote machine where to place the display on your machine.
Finally type
and hit return again.
This will enable the sybyl software and allow access to all the SYBYL components such as MOPAC, HINT, MOLCAD, UNITY, SITE ID, FUGUE, GENEFOLD and all the rest.
Sybyl has a LARGE number of components.
Here are preparative things you need to perform prior to running VolSurf. You must copy two files into your home directory like so:
cp $VOLSURF_DIR/volsurfrc $HOME/.volsurfrc
chmod 644 $HOME/.volsurfrc
cp $VOLSURF_DIR/plotGridrc $HOME/.plotGridrc
chmod 644 $HOME/.plotGridrc
For access to CombiLibMaker and CONCORD you must first perform the following:
-Login as yourself
-Type "trigo -shell sybyl"
-Type "cp $TA_ROOT/partner/.rshlogin_all $HOME/.rshlogin"
-Type "exit" This gets you out of the Trigo shell.
-Edit the .rshlogin file to uncomment the platform relevant lines eg HP, LINUX or SGI.
-N.B. Only uncomment one platform at a time. If you migrate to another platform you will need to edit .rshlogin with each migration commenting the old and uncommenting the new.
UNIX RASMOL, an excellent molecular viewer, may be started from a UNIX command line by typing
and hitting return. On PC and MACs the program code is also available and can be installed at your convenience.
Creating a MOLSCRIPT image from RASMOL is a four step process.
First retrieve a molecular structure in PDB format.
Second, scan the file for secondary structure elements using the program DSSP by typing:
This creates an output file (xxx.dssp)
Third convert the dssp output into molscript format by typing
and follow the prompts for entry of the dssp output file (xxx.dssp), the chains to be modeled(usually all or "*"), and the name of the output file (xxx.in) and the name of the pdb file (xxx.pdb).
Fourth run molscript. Type:
This produces a molscript file in Postscript format which can be printed or viewed with any Postscript capable device. The image is static.
Biomolecular Computing Resource Created by ESH Modified July 30, 2007 13:17