User 870ab5b546
28-07-2015 17:18:43
Consider the following 3D structure representing chair cyclohexane.
<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x3="-0.8287333333333333" y3="-0.7503166666666666" z3="0.96" mrvMap="1"/><atom id="a2" elementType="C" x3="-2.2619333333333334" y3="-0.5131166666666667" z3="1.3814" mrvMap="2"/><atom id="a3" elementType="C" x3="-3.2236333333333334" y3="-0.6876166666666665" z3="0.22699999999999998" mrvMap="3"/><atom id="a4" elementType="C" x3="-2.8378333333333337" y3="0.16698333333333326" z3="-0.96" mrvMap="4"/><atom id="a5" elementType="C" x3="-1.4046333333333334" y3="-0.0701166666666666" z3="-1.3814" mrvMap="5"/><atom id="a6" elementType="C" x3="-0.44303333333333317" y3="0.10428333333333328" z3="-0.22700000000000004" mrvMap="6"/><atom id="a7" elementType="H" x3="-0.20690113008507854" y3="-0.4174305528026674" z3="1.7910304123195164"/><atom id="a8" elementType="H" x3="-0.7772333614390399" y3="-1.7850109607890279" z3="0.6210966648061494"/><atom id="a9" elementType="H" x3="-2.5025003530975733" y3="-1.2961992732991203" z3="2.100433476405288"/><atom id="a10" elementType="H" x3="-2.324471024245207" y3="0.534628101970784" z3="1.6753726807175553"/><atom id="a11" elementType="H" x3="-3.12624442109946" y3="-1.723524194583343" z3="-0.0978245578454045"/><atom id="a12" elementType="H" x3="-4.187128076033667" y3="-0.3131633206668981" z3="0.5727782128162442"/><atom id="a13" elementType="H" x3="-3.459615839563311" y3="-0.16591442079901042" z3="-1.7910629339827457"/><atom id="a14" elementType="H" x3="-2.8893688162933064" y3="1.2016772005062233" z3="-0.6211007594713556"/><atom id="a15" elementType="H" x3="-1.342033552657236" y3="-1.117826165450826" z3="-1.6754851468822427"/><atom id="a16" elementType="H" x3="-1.1640604098562506" y3="0.7130560048082611" z3="-2.10033340104944"/><atom id="a17" elementType="H" x3="-0.5404406406528928" y3="1.1401811820616747" z3="0.09784990915921019"/><atom id="a18" elementType="H" x3="0.5204634083326185" y3="-0.2701389509754751" z3="-0.572806277866768"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"/><bond atomRefs2="a1 a6" order="1"/><bond atomRefs2="a2 a3" order="1"/><bond atomRefs2="a3 a4" order="1"/><bond atomRefs2="a4 a5" order="1"/><bond atomRefs2="a5 a6" order="1"/><bond atomRefs2="a1 a7" order="1"/><bond atomRefs2="a1 a8" order="1"/><bond atomRefs2="a2 a9" order="1"/><bond atomRefs2="a2 a10" order="1"/><bond atomRefs2="a3 a11" order="1"/><bond atomRefs2="a3 a12" order="1"/><bond atomRefs2="a4 a13" order="1"/><bond atomRefs2="a4 a14" order="1"/><bond atomRefs2="a5 a15" order="1"/><bond atomRefs2="a5 a16" order="1"/><bond atomRefs2="a6 a17" order="1"/><bond atomRefs2="a6 a18" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
If I type an atom symbol and then click on an H atom, the z-coordinate of the original atom is preserved. This behavior is good. However, if I type the name of a shortcut group in the abbreviated groups dialog, then click on an H atom, the z-coordinate of the original atom is *not* transferred to the new shortcut group or its attachment point. This behavior is bad.
MarvinSketch shows the correct behavior, BTW.
This bug is fairly high priority for me. We have students who try to draw compounds in their 3D structures, and while they can always draw out the entire structure of the shortcut group, that's tedious. Plus, it's not possible to tell by visual inspection that the z-coordinate of the shortcut group has been set to 0, unless you know to rotate the structure.