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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}