MAGE is a program that reads "scripted" or "authored" interpretations of how to graphically render or display a structure. The files that MAGE reads are called Kinemages. These can be quite nice, but the "stock" rendering done from raw structure data can sometimes be too memory-intensive to view from large structure files. MAGE is used by many educators, as files can have extensive annotations in them which are presented concurrently with the structure. MAGE for UNIX is new and works great compared to its Mac and PC variants that have trouble with large files.
NOTE: MAGE has memory restrictions that vary from system to system. Entrez is capable of making Kinemage files that are TOO BIG for some implementations of MAGE.
In MAGE, there are clusters of buttons on the right side of the structure
image. These buttons turn parts of the structure on or off, and are scripted
into the generated Kinemage file by Entrez. These buttons can be used to turn
on or off side-chains (residues), backbones (real = all atoms; virtual =
alpha-carbons), ions or small molecules (hets) if they are present in your
structure. The second cluster of buttons from the bottom of the button list is
a set of "master" buttons that you should experiment with first. A button on
the very bottom marked "Animate" - if present - can be used to show an
animation, if it has been rendered for you by Entrez (e.g. try accession
5HVP).
If you don't have a copy of MAGE executable on your system, or need the
latest version, you can get the executable program from the
authors (Robert M. Weiss and David C. Richardson) via
Anonymous ftp. Please
familiarize yourself with the program and its demonstration files
before using it to view Entrez-generated Kinemages.
Yes, but currently only in the MAGE-Version for Windows or on the Macintosh.
Unix versions don't seem to have memory settings.
Under Windows, MAGE memory is adjustable within
the very first window that appears in MAGE. There is a button that says
"atom limit". By default this setting is 4,000 but try 10,000.
(15000 seems close to its absolute maximum). WWW users who are trying to
launch MAGE under Windows should note that this can be done before hitting
the "proceed" button in MAGE. Should the available memory settings not allow
for viewing of big structures with the complexity desired, we recommend to
use another viewer like Cn3D or RasMol.
To change MAGEs memory settings on the Mac, use the System Finder. Select the
MAGE Icon, then pick the File|Get Info option from the menus. There will be a
box with memory settings at the bottom. Adjust these to 4 Meg or more, but ONLY
if you have that much memory to spare.
Absolutely. Chop out parts you don't want in a text-editor if you need to make
it smaller.
How do I use an NCBI-generated Kinemage file?
How can I obtain MAGE?
How do I set up my WWW Browser to Launch MAGE?
If you are using WWW Entrez, you can set-up your WWW browser to launch
the 3D viewing sofware automatically. See our guide to
installing a structure viewer for details.Can I adjust the amount of memory availiable to MAGE?
Can I edit the Kinemage file to make it smaller?
Revised April 16 1998, Comments and questions to:
info@ncbi.nlm.nih.gov