(fwd) Molecular Modelling on a PC

Brad Isbister longshot at chem.duke.edu
Tue Jul 5 18:54:20 EST 1994

In article <CsHBD6.8s at osuunx.ucc.okstate.edu>,
Cyber Stud <kage at osuunx.ucc.okstate.edu> wrote:
>   I dealt with a program called kinemage or magekine or something like
>that a while ago.  I can't tell you too much about it except that it at
>least displayed models on a pc...both and ibm clone and a mac (two diff
>versions).  It seemed interesting enough to spend some time on but I 
>dropped it when I determined that it couldn't read PDB formated files
>from brookhaven.                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   
                                                Not accurate!

	More message on PC vs workstation modeling

>Ross Keener
>v369 at rem.re.uokhsc.edu

Kinemage was written by David Richardson here at Duke.  It is not a
modelling program, but rather a very flexible and useful tool for
visualizing structural information.  And it makes input files with the
utility Prekin, which reads PDB files!  Kinemage is supported on Macs
and PC clones at least.  I don't know if it has been ported to other

Kinemage allows for animation of views between several structures:
eg bound vs unbound structures, structures at different pH or temp,
and so on.  You can also include labels and buttons to un/display
particular features.  Any degree of rotation and magnification can be
recalled as a view.

Another feature of Kinemage is that the user can measure distances,
angles, dihedrals, and improper dihedrals with the mouse.  That makes
it a great teaching tool.  Kinemage is used in undergraduate and grad
courses here to illustrate protein & nucleic acid structure and

My own work relates to the binding of carbohydrates to proteins.  I
have used Kinemage to take PDB files of protiens with & without ligand
and animating them.  I made views with C-alpha backbone + ligand from
several angles, then zoomed in on the specific residues in the binding
loops.  I animated the binding event and made buttons for sidechain
atoms so that the binding can be viewed without the clutter of
sidechains for a 'big picture' of what's moving, or a detailed view of
how each sidechain participates in the binding.

Kinemage can display any kind of data which can be represented by
arbitrary groups of points and lines.  If you've got proteins or
nucleic acids, the Prekin program will usually be able to give you the
view you want with just a few clicks of the mouse.  If you want to use
the kinemage in a lecture or presentation, all it takes is a little
cleaning up with your favorite editor.

Kinemage can be retrieved from any of several ftp sites.  Give archie
a try for the site nearest you!

I don't have any relationship with the Richardson lab, and the
graphics are not publication quality (I use Sybyl, Molscript, or
RasMol for that), but it's great as a data analysis tool when you're
looking for relationships between different structural features.


Brad Isbister		Computational/Physical Biochemistry
Duke University		longshot at canada.chem.duke.edu

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