ABCC : Application's document Page

SYBYL At ABCC
Name: 
SYBYL
Version(s): 
7.0
Category: 
Molecular Modeling; Molecular Visualization
Author(s)/Vendor(s): 
Tripos Inc. 
1699 South Hanley Rd. St. Louis, MO 63144
Phone 800-323-2960 314-647-1099 Fax 314-647-9241 
info@tripos.com
www.tripos.com
Program Description: 
SYBYL is a general use molecular modeling and visualization package. It provides 
essential construction, editing, and visualization tools for both large and 
small molecules.
               
Building and Editing  
Molecular structures can be entered from a variety of sources.  SYBYL reads many 
formats, including MDLi MOL and SD, Cambridge  Structural Database, Protein 
Data Bank, and SMILES. Direct entry of structures is also possible using SYBYL's 
sketcher or 3D building Tools.                       

Computation 
Geometry optimization (minimization) is performed via molecular  mechanics or 
quantum mechanical (interface to MOPAC) methods.  SYBYL offers a variety of force 
fields (Tripos, Amber, MM2 and  MMFF94) as well as several options for computing 
or importing atomic charges. Several algorithms are available for generating 
 solvent models. Geometric features such as planes, normals, and  centroids can be 
defined. Distance, angle, and torsion constraints  for minimization can be 
keyed to individual atoms or geometric features.

Molecular Spreadsheet
 SYBYL contains built-in tools for analysis of molecular structure,  as well 
as the interactive Molecular Spreadsheet. The Molecular Spreadsheet (MSS) organizes 
the analysis of molecule sets. Rows  represent molecules, and columns contain 
related metrics such as molecular weight, topographical data, energies, and 
biological activity. Over 60 built-in metrics are available, with others 
provided by additional modules.

Visualization
 Molecules can be displayed as lines, sticks, ball-and-stick, or spacefilling 
spheres. Colors, labels, depth cueing, shading, stereo view mode, and Z-clipping 
can be readily changed through the toolbar. Volume displays, contours, 
grids, and dotted surfaces provide the ability to visualize molecular 
properties. Views can be annotated with arrows and text, either in 2D or with 
elements  that rotate and translate with the molecules. 

Customization
SYBYL enables custom design methods via the SYBYL Programming  Language (SPL).
Computer platform(s): 
SGI Irix
Linux
Location: 
/usr/local/fbscapp/sybyl
Access: 
Account at ABCC's SGI systems is required to run Sybyl. NCI scientist can also run 
it directly on their SGI or Linux workstation via a /usr/local/fbscapp 
filesystem mounted from ABCC's servers (no ABCC account is required in this mode of operation).

Set your environment for Sybyl with the following commands:
  setenv TA_ROOT /usr/local/fbscapp/sybyl
  setenv TA_BROWSER /usr/bin/X11/netscape
  source $TA_ROOT/lib/.login
Then type the following to invoke sybyl:
  sybyl

Note: the second setenv command above lets you set the env variable TA_BROWSER,
 so that sybyl can invoke the book-shelf using the Netscape browser.
Documentation: 
Available in the html format in the directory
/usr/local/fbscapp/sybyl/TriposBookshelf
    
If you are on the ncifcrf.gov network, the following URL will also work for you 
- http://ncisgi.ncifcrf.gov/tripos/. Note, that the "Search the Tripos Bookshelf" 
functionality works only with the browser run on ncisgi.ncifcrf.gov.
Web Site: 
http://www.tripos.com/sciTech/inSilicoDisc/moleculeModeling/sybase.html
ABCC Contact Person: 
Sarangan Ravichandran
sravi@ncifcrf.gov
301-8461991
Created By: 
miaskiew
Created Time: 
2001-10-22
Updated By: 
miaskiew
Updated Time: 
2006-02-23
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