User 870ab5b546
23-05-2008 14:37:04
In the following compound, if I select the N and choose Structure -> Add -> Add Explicit Hydrogens (Marvin 5.0.3), it alters the xyz coordinates of the N atom in an atrocious way. It should not alter them at all.
However, the xyz coordinates of the N atom are not altered if I don't select any part of the molecule.
-- Bob
However, the xyz coordinates of the N atom are not altered if I don't select any part of the molecule.
-- Bob
| Code: |
| <?xml version="1.0" ?> <cml> <MDocument> <propertyList> <property dictRef="viewEulerAngles" title="viewEulerAngles"> <array size="3" dataType="xsd:double">2.00029640855057 0.09330289234985761 -2.914221041823679</array> </property> <property dictRef="scale" title="scale"> <scalar dataType="xsd:double">42.0</scalar> </property> </propertyList> <MChemicalStruct> <molecule title="k08097 - P21/c" molID="m1"> <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31 a32 a33 a34 a35 a36 a37 a38" elementType="N N O O O O C H C H H C H H C H H C H C H C H H C H H C C H C H C H C H C H" formalCharge="1 1 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0" x3="5.1882 4.9301 4.3763 1.4667 5.5783 4.6344 5.7892 6.1806 6.886 7.6438 6.529 7.3239 8.2354 7.3195 6.2982 5.9617 6.7207 4.5454 4.1363 3.5941 3.326 2.3607 2.5996 1.9394 0.248 -0.1134 0.4066 -0.7383 -1.5082 -1.3977 -2.4362 -2.9573 -2.6014 -3.2468 -1.8214 -1.9209 -0.8953 -0.3617" y3="3.9261 4.2511 5.1283 4.8834 3.501 5.3837 3.6496 2.7297 4.7061 4.3286 5.4919 5.0909 4.7533 6.0745 4.4336 5.0967 3.6895 3.7255 2.8175 4.6509 5.4202 3.9126 3.2508 3.4344 4.3026 3.708 3.7604 5.398 5.9556 5.6511 6.9532 7.3253 7.4051 8.0746 6.876 7.1948 5.8822 5.528" z3="7.6626 11.248 8.0071 8.1146 11.9554 11.5722 8.9863 9.0075 9.2048 9.718 9.6896 7.78 7.5924 7.6678 6.8389 6.1853 6.341 9.8865 9.9768 9.1099 9.6897 8.6431 7.9467 9.4007 7.677 8.3812 6.8639 7.3767 8.3965 9.2895 8.1191 8.8209 6.819 6.6248 5.8051 4.9157 6.0836 5.3819" /> <bondArray> <bond atomRefs2="a1 a3" order="1" /> <bond atomRefs2="a1 a7" order="1" /> <bond atomRefs2="a1 a15" order="1" /> <bond atomRefs2="a2 a5" order="1" /> <bond atomRefs2="a2 a6" order="2" /> <bond atomRefs2="a2 a18" order="1" /> <bond atomRefs2="a3 a20" order="1" /> <bond atomRefs2="a4 a22" order="1" /> <bond atomRefs2="a4 a25" order="1" /> <bond atomRefs2="a7 a8" order="1" /> <bond atomRefs2="a7 a9" order="1" /> <bond atomRefs2="a7 a18" order="1" /> <bond atomRefs2="a9 a10" order="1" /> <bond atomRefs2="a9 a11" order="1" /> <bond atomRefs2="a9 a12" order="1" /> <bond atomRefs2="a12 a13" order="1" /> <bond atomRefs2="a12 a14" order="1" /> <bond atomRefs2="a12 a15" order="1" /> <bond atomRefs2="a15 a16" order="1" /> <bond atomRefs2="a15 a17" order="1" /> <bond atomRefs2="a18 a19" order="1" /> <bond atomRefs2="a18 a20" order="1" /> <bond atomRefs2="a20 a21" order="1" /> <bond atomRefs2="a20 a22" order="1" /> <bond atomRefs2="a22 a23" order="1" /> <bond atomRefs2="a22 a24" order="1" /> <bond atomRefs2="a25 a26" order="1" /> <bond atomRefs2="a25 a27" order="1" /> <bond atomRefs2="a25 a28" order="1" /> <bond atomRefs2="a28 a29" order="A" /> <bond atomRefs2="a28 a37" order="A" /> <bond atomRefs2="a29 a30" order="1" /> <bond atomRefs2="a29 a31" order="A" /> <bond atomRefs2="a31 a32" order="1" /> <bond atomRefs2="a31 a33" order="A" /> <bond atomRefs2="a33 a34" order="1" /> <bond atomRefs2="a33 a35" order="A" /> <bond atomRefs2="a35 a36" order="1" /> <bond atomRefs2="a35 a37" order="A" /> <bond atomRefs2="a37 a38" order="1" /> </bondArray> </molecule> </MChemicalStruct> </MDocument> </cml> |