describes for you
STING : PDB_Viewer
V 2.1
| Brazil | http://www.cbi.cnptia.embrapa.br/ |
| Brazil | http://asparagin.cenargen.embrapa.br/SMS/ |
| USA | http://trantor.bioc.columbia.edu/SMS/ |
| USA | http://mirrors.rcsb.org/SMS/ |
| Spain | http://www.es.embnet.org/SMS/ |
| Argentina | http://www.ar.embnet.org/SMS/ |
| Japan | http://gibk26.bse.kyutech.ac.jp/SMS/ |
laboratory and Columbia University,
Barry Honig's Laboratory.
What is STING?
Sequence to Graphics & Graphics to Sequence Easy Link
Searching for the right PDB file
Browse and find Local PDB-format files
Links to important Databases and servers
Supported Platforms
Supported Input Formats
Instructions for downloading STING
Using STING
as a Web/MIME Helper Application Known bugs
What you can do with
STING: STINGpaint - our tool for
SEQUENCE coloring
STING: Charge complementarity on molecular interfaces
STING: Protein/DNA Interface and Structural Waters
STING: Ligand Pocket and Coordinating Residues
STING: Enzyme/Inhibitor Interface and Structural Waters
| PC ONLY features are written in this way: within yellow box! |
Special attention
in STING is given to MacroMolecular INTERFACE analysis.
STING's Sequence to Graphics & Graphics to Sequence Easy Link
STING shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.
Sequence and Graphics frames are interconnected so that the user can have control of
both types of information; With only one stroke
("click" ) on the chosen sequence residue, a user of the
STING PDB Viewer can get a visual presentation of the 3D position
of that residue within the Macromolecular 3D structure!
| A user can search the Graphics Frame and ask questions such as: which residue is at a particular spot pointed by the mouse within a 3D frame? |
In addition, the user has a complete information about a
sequence: numbering, gaps and also PDB defined
secondary structure regions [Helices (red lines below the
sequence) and Extended Sheets (blue lines below sequence)].
Browse and find Local
PDB-format files
The user can search for the right PDB file by using 3DB Browser. In
this case search is done on BNL/PDB.
Note: the user should realize that search on BNL/PDB will also
offer "Sting It" option once right file is found. If that option is
used, the BNL/PDB copy of that file is accessed.
Alternatively, after using 3DB Browser, the user can come back to its local site and simply type in 4 letter code of the right PDB file into the "PDB Code from local copy of entire PDB:" field and press "Enter" key on the keyboard. This will significantly speed up STING presentation, as PDB file will be accessed on local server.
The user can also browse local directories and search for the any PDB format file.
If the user knows exact path and file name, this path and file name should be entered into:"Local PDB file Name:" field, and then press "Sting It" button below that same field.
If user does not know exact path and/or file name, "Browse" button should be pressed and file name should be found. Once Browse option is completed, the user is expected to press "Sting It" button just below the "Browse" button. New browser will be opened and STING will display content of that particular file.
Important Note for PC users: If the user wants to reload LOCAL file,
or the user resizes the browser, STING will show netscape error msg. We are
working on this bug now. However, the user can explore all STING features and
analyse local files in all but this case!reload LOCAL file,
or the user resizes the browser, STING will show netscape error msg. We are
working on this bug now. However, the user can explore all STING features and
analyse local files in all but this case! SGI version of the STING is working
without any problems within the frame.
STING's Working Area Frames
The STING PDB Viewer has
4 frames: The Working area of the browser is divided into
upper left: a Graphics Frame,
upper right: Links and specific Chime script commands
(STING's Control Frame), and
middle right: PDB Info Frame with information on chains, ligands,
ions and water molecules present in the PDB entry
lower frame: Sequence Frame which contains the linear
protein sequence color coded with respect to Hydrophobicity and
charged groups!
The Sequence Frame also shows numbering of the residues in the
sequence, gaps in the PDB sequence, chain identifier and
secondary structure elements identifier. Each residue in the
Sequence Frame is "clickable", resulting in CPK presentation of its
position in 3D in the Graphics Frame. Blue and Red lines below the
sequence are also "clickable" resulting in graphical RIBBON
presentation of the specified sequence region!
STING's Status Frame is the browser's link-indicating area at the lower browser border.
The user can see sequence complete identification while sliding the mouse over the sequence in the
STING's Sequence Frame, or while clicking the mouse's left button over atoms in STING's
Graphics frame.
STING's Control Frame has a number of pre-defined CHIME Scripts to be
executed after pressing a button of choice; One can easily:
**color code all charged residues,
**color code chains,
**select and display the ligand and only water molecules in vicinity of the ligand;
**select and display ligand pocket (residues within 2 Angstroms
from the ligand) and finally,
**display (again using a single stroke = click on the button) the interface between two
chains!
Known bugs:
This software is under continuous development and we
expect bugs to be found...Please contact us if you find any problem!
Reloading LOCAL file (other than files from local copy of the entire PDB, which are stored in the /pdb directory), or resizing the browser when Local files are analyzed by STING, will produce netscape error msg. We are working on this bug now.
PC ONLY: When the user starts with the STING entry page (where the options for
the right PDB file are posted to be filled in) and opts to use:
"Protein Data Bank 3DB Browser", then follows search options and finally
opts for the "Sting It" button on the 3DB Browser page, STING will attempt to
open in the frame, rather than on separate browser window. This in turn, will
couse STING scripts not to function properly. Avoid that sequence of events,
and all will be functioning properly. We are working on procedure that will
always open a new browser for STING. SGI version works fine within the frame!
Note: The user should check the content of the /tmp directory on STING server side and remove all reminiscent files created by STING. We are working on procedure to automatize this process.