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type=chemistry
textarea="data file scriptinput scriptoutput pre post"
iEdit="pre post"

:Select some atoms of a molecule

<p>
  We present a 3D interactive molecule (Jmol) and we ask to select certain atoms.
</p><p>
  To build an exercise with this model, just give the structure file and indicate the atoms to be selected.
</p><p class="wims_credits">
  Author of the model: Yves Noël & Bernadette Perrin-Riou <yves.noel@upmc.fr>
</p>
:%%%%%%%%%%%%%%%%%      ATTENTION      %%%%%%%%%%%%%%%%%%%%

Remove the above header if you destroy the model tags! (The lines starting
with a ':'.) Otherwise the exercise might not be taken back by Createxo.

:%%%%%%%% Sample parameters to be redefined %%%%%%%%%%%%%%%%%

:\title{Select in 3D}
:\author{Yves, Noël ; Bernadette, Perrin-Riou}
:\email{yves.noel@upmc.fr}
:\credits{}

:MDMol file
\text{file=xxx
Jmol version 11.7.31  2009-03-28 16:42
EXTRACT: visible
 24 25  0  0  0
 -3.380413 -1.127236 0.5733036 H
 0.9668296 -1.073742 -0.819822 N
 0.0567293 0.8527195 0.3923156 C
 -1.375174 -1.021224 -0.057055 N
 -1.261501 0.2590713 0.5234135 C
 -0.306833 -1.683633 -0.716934 C
 1.1394234 0.1874122 -0.27009  C
 0.5602627 2.0839095 0.8251589 N
 -0.492679 -2.818055 -1.209473 O
 -2.632807 -1.730396 -0.006095 C
 -2.230133 0.7988624 1.089973  O
 2.549699  2.9734976 0.6229589 H
 2.0527434 -1.736088 -1.493128 C
 -2.480771 -2.726952 0.4882631 H
 -3.008904 -1.902525 -1.049802 H
 2.9176102 -1.848151 -0.785786 H
 2.378786  -1.121191 -2.374365 H
 1.7189878 -2.748991 -1.843920 H
 -0.151845 3.0970047 1.5348347 C
 1.8934095 2.1181242 0.4193193 C
 2.2861252 0.9968439 -0.244029 N
 -0.168702 4.043655  0.9301094 H
 0.3535322 3.297906  2.5177748 H
 -1.207449 2.7537594 1.7203048 H
 24 19  1
 22 19  1
 20 21  1
 20 12  1
 19 23  1
 19  8  1
 18 13  1
 15 10  1
 13 17  1
 13 16  1
 11  5  1
 10 14  1
 10  4  1
  9  6  1
  8 20  1
  7 21  1
  6  2  1
  5  3  1
  4  6  1
  4  5  1
  3  7  1
  3  8  1
  2 13  1
  2  7  1
  1 10  1
}

:Applet size, in pixels, width x height

\text{size1=340x220}

:Atoms to click on (one of the lines will be random)

\matrix{atom=_N
_O
_C}

:Instructions specific to each previous line

\matrix{names=nitrogen
oxygen
carbon}

:%%%%%%%%%%%%%%
\text{cnt=\atom[;1]}
\integer{cnt=items(\cnt)}
\text{sel=randint(1..\cnt)}
\text{picked=\atom[\sel;]}

\text{name=\names[\sel;]}
:%%%%%%%%%%%%%%

:Text before the applet
Use the word \name to display the atom picked.
\text{pre=Select all the <strong>\name</strong> atoms.}

:Text after the applet
\text{post=<i>Check that your browser's zoom is on the normal size.</i>}

:Jmol script to perform when presenting the exercise
\text{scriptinput=select all;color atoms yellow; select none;}

:Jmol script to perform when presenting the response
\text{scriptoutput=}



:%%%%%%%%%%%%%% Nothing to modify until statement %%%%%%%%%%%%%%%%


\statement{
  <div class="instruction">\pre</div>
  <div class="wimscenter">
    \embed{reply 1, \size1

\scriptinput
\scriptoutput}
  </div>
  <div class="post">\post</div>
}

:%%%%%%%%%%%%% Nothing to modify after. %%%%%%%%%%%%%%%%%5

\answer{}{\picked;\file}{type=jmolclick}