Cleaning up a metallocene in 3D

I created a dimethylsilyl(bisindenyl)zirconium dichloride in MarvinSketch 5.0.1.





Some points that need adjustments:


1. Can I force indenyl groups to be in a plane? Now 6-membered part is bent of the indenyl plane.


2. In 2D presentation of the 5-ring there is a real ring representing aromaticity. In 3D the ring representing aromaticity is changed to a dash lines. Even more the dashed bonds are in different plane than 5-ring. Dashed bonds actually consists of two "allylic" bonds, which are on opposite sides of the 5-ring or atleast it looks like it when rotating the structure. Can I get rings to represent 5-ring aromaticity in 3D like in 2D?


3. Or can I flatten the 3D to a 2D presentation so that I get aromaticity rings to 5-rings and the structure does not braek apart?





Look at the example attachment picture to get the idea what I would like to copy/paste to documents and presentations. Is this possble with Marvin?








Source

Code:

<?xml version="1.0" ?> <cml> <MDocument>   <propertyList>     <property dictRef="viewEulerAngles" title="viewEulerAngles">       <array size="3" dataType="xsd:double">1.2353525662021776 0.8093816465412876 -0.2030891024657812</array>     </property>   </propertyList>   <MChemicalStruct>     <molecule 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"           elementType="C C C C C C C C Zr Si C C Cl Cl C C C C C C C C C C X X"           sgroupRef="sg2 sg2 sg2 sg2 sg3 sg3 sg3 sg3 0 0 0 0 0 0 0 sg3 0 0 0 0 0 0 sg2 0 0 0"           x3="-1.1392212020751584 -2.3120238539022875 -0.6817363742848138 -0.14599757496330848 -1.351450075188996 -0.6414958069205567 -2.030086775527019 -2.4634165235102774 -1.6162271579479996 -0.06135384880560372 1.6986495811274542 -0.5973345854120775 -4.071556742211091 -1.3738550409153325 -1.2133378048514665 -0.23206559927671128 1.058780346876998 1.2001289227402858 0.07214419171259176 -4.451348112072072 -4.246480697455474 -3.0362855395716286 -2.0592411312558037 -3.460814402503832 -1.2676440272962743 -1.343702956084712"           y3="3.0190495335700076 2.282317872291162 0.910643582657726 2.185816732287472 2.943816296884664 0.93945753573354 0.8982221677320483 2.1192153668576807 2.3571571365136057 0.07215591772281289 0.008532299095068497 -1.6059139463991727 3.370606152413131 5.006135729484407 4.103705835968392 2.248769143245564 2.7787881544961 4.003829771803521 4.655820787256857 1.5672509492252558 0.2932888084345797 -0.00993654954154049 0.9974733438140834 2.561651527843371 1.8790602129240903 1.8298961020906994"           z3="2.1066575980685696 2.1587400628618982 1.3401439080558788 1.6085121570269505 -2.181156793640689 -1.3536219802476785 -1.588629365675778 -2.0869150142911987 -0.003977475276255624 -0.00738978024364042 0.04977760355728476 -0.06238257991500265 -0.014354382949948114 0.003389918832816011 -2.968551448337199 -1.6964443414753516 -1.9087779840954366 -2.5927427077183003 -3.134628964311572 3.0390174159872405 2.4682453059028573 1.809768716382268 1.6557501725846333 2.925088407673256 1.773960779719586 -1.7813534990661388"           />       <bondArray>         <bond atomRefs2="a1 a2" order="A" />         <bond atomRefs2="a1 a4" order="A" />         <bond atomRefs2="a23 a3" order="A" />         <bond atomRefs2="a3 a4" order="A" />         <bond atomRefs2="a5 a8" order="A" />         <bond atomRefs2="a16 a6" order="A" />         <bond atomRefs2="a6 a7" order="A" />         <bond atomRefs2="a7 a8" order="A" />         <bond atomRefs2="a10 a3" order="1" />         <bond atomRefs2="a10 a6" order="1" />         <bond atomRefs2="a10 a11" order="1" />         <bond atomRefs2="a10 a12" order="1" />         <bond atomRefs2="a9 a13" order="1" />         <bond atomRefs2="a9 a14" order="1" />         <bond atomRefs2="a15 a5" order="1" />         <bond atomRefs2="a15 a19" order="2" />         <bond atomRefs2="a16 a17" order="1" />         <bond atomRefs2="a17 a18" order="2" />         <bond atomRefs2="a18 a19" order="1" />         <bond atomRefs2="a5 a16" order="A" />         <bond atomRefs2="a2 a24" order="1" />         <bond atomRefs2="a20 a21" order="1" />         <bond atomRefs2="a20 a24" order="2" />         <bond atomRefs2="a21 a22" order="2" />         <bond atomRefs2="a22 a23" order="1" />         <bond atomRefs2="a2 a23" order="A" />         <bond atomRefs2="a25 a9" convention="cxn:coord" />         <bond atomRefs2="a26 a9" convention="cxn:coord" />       </bondArray>       <molecule id="sg1" role="MulticenterSgroup" molID="m2"          atomRefs="a1 a27 a3 a4"  center="a28"         />       <molecule id="sg2" role="MulticenterSgroup" molID="m3"          atomRefs="a1 a2 a23 a3 a4"  center="a25"         />       <molecule id="sg3" role="MulticenterSgroup" molID="m4"          atomRefs="a5 a16 a6 a7 a8"  center="a26"         />     </molecule>   </MChemicalStruct> </MDocument> </cml>

Hello,





1. You are right, the indenyl groups should be in a plane after 3D cleaning. Thank you for the bug report we are working on this problem.





2. We are planning to improve metallocene drawing quality in the next major releases: that will include the circle in the ring instead of dashed lines in 3D representation.





3. At the moment there is no possibility to get that kind of 3D to 2D conversion (projection).





Best regards,


Erika.