Re: [Jmol-users] features in applet don't match application

[Philip Bays]

This might be a programming nightmare, but I will give it a shot.  When 
the applet loads the file, it "knows" what atoms are present.  Is it 
possible to make the contextual menu a listing of those atoms.   Thus, 
if the user was working with proteins, there would be the usual 
C,H,O,N,S and then any metal or other hetero atoms listed from which 
the selection could be made.    On the other hand, if the structure was 
an inorganic cluster, a different set of atoms would be in the 
selection menu.

Just a thought :)

Phil

J. Philip Bays
Department of Chemistry and Physics
Saint Mary's College
Notre Dame   IN  46556
[EMAIL PROTECTED]


On Jan 26, 2004, at 11:48 AM, Jan Reichert wrote:

Hi Miguel,
a snowbird is back :-)

My latest venture is displayed at :
http://www.saintmarys.edu/~pbays/Complexes/Complexes.htm.
Obviously, we are doing some meta- ligand chemistry in my intro 
course
:)

Looks great!

Yes, Jmol looks great.

I am going to try to drag you into the 'colors' discussion ... What 
color
do you think that Magnesium should be?

In RasMol2.7 the colors are defined as shown in
http://www.imb-jena.de/~jr/VisAnPred/RasMol/Myoglobin/img18.gif
other color schemes are
http://www.imb-jena.de/~jr/VisAnPred/PSEinsightII.gif
http://www.imb-jena.de/~jr/VisAnPred/PSEmolscript.gif
http://www.imb-jena.de/~jr/VisAnPred/PSEmolmol.gif
http://www.imb-jena.de/~jr/VisAnPred/PSEspdbv.gif
http://www.imb-jena.de/~jr/VisAnPred/PSEchimera.gif
http://www.imb-jena.de/~jr/VisAnPred/PSEprepi.gif
http://www.imb-jena.de/~jr/VisAnPred/PSEjmol.html
this kind of green as used in PSErasmol.gif for Mg is OK for me, but I 
would like to alter the RasMol scheme to

select carbon
color [0,255,0]
and to compensate Cl has to change to

select chlorine
color [153,255,102]
and additionally I prefere P in magenta

select phosphorus
color magenta


If you can, please send me 1 paragraph (no more!) that tells me about 
the
interesting 'bonding' of ferrocene :-)

metallocene: interaction of  the pi-electrons from two C5H5 with the d 
of the transition metal
http://www.ncl.ox.ac.uk/mom/ferrocene/ferrocene.html

Regards, Jan



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