                   Jim's Molecule Renderer (Ball n Stick)
                                                by Jim Vito


        This is a program to accompany jmr.exe. I would suggest placing it
in a separate directory then jmr. To use the application follow the directions 
for jmr.exe. Type jmr_bs to get a parameter listing.
I have included a library of pdb files. Use BABEL and convert the pdb's
to xyz. The xyz files must then be converted manually to .coo type.

If you have any questions ... contact javito@netcom.com.

Configuration files: (described)
ATOMIC.DEF
************************************************
H .37 .90 .2 .57          - atom type  radius red green blue
C .40 .97 .20 .18                  (color values range from 0.00 - 1.00)
N .68 .1 .999 .123
O .66 .823 .1 .845
P 2.2 0 0 .555
S 1.6 .8 .8 .122
************************************************
VALID.JJV
************************************************
VIEWER 500 500 1000                  - viewer position x y z
AMBIENT .2977 .2977 .2977            - ambient light intensity red green blue
LIGHT .44 200 0 1200 1 1 1      -light sources intensity x y z red green blue
LIGHT 0 300 200 1200 1 1 1
LIGHT 0 700 -500 1200 1 1 1
LIGHT 0 1800 0 1200 1 1 1
LIGHT 0 0 1300 1200 1 1 1
PHONG_KS .9                     - specular eflection coefficient 
PHONG_N 20                      - phong shading control parameter
BACKGROUND 1 1 1                - background color red green blue
OBJECT_DISTANCE 480       - distance to set molecule back in scene.(see below) 
CYLINDER_RADIUS_AND_COLOR .15 .875 .604 .96 
BOND_DISTANCE_THRESHOLD 1.6   - maximum distance of bonded atoms. (angstroms)

I have written a full lighting and color design app for windows.
This new application will allow you to specify atom radius, color, and
lighting characteristics through a graphical interface.

******************************************************************************
Feel free to distribute this file in its complete form. If you plan to use 
the output files in a presentation, journal, business or commercial purpose..
.. You must obtain a registered copy.
$30 will get you a registered copy.
Registered users will also get a discount on future revisions and upgrades of 
this package. 

If you find this program useful... or would like to see future improvement..
any Donations will be gladly appreciated. 
If you would like the application modified for a specific application please 
let me know. 

Thanks.                        
Jim
javito@netcom.com
378 E. Duane Ave.
Sunnyvale, CA 94086
                        


