invisible atom

User 870ab5b546

19-09-2014 18:38:23

How could a student have used MarvinSketch to draw the following structure, which includes an invisible pseudoatom? I'm just trying to figure out how he did it.


<?xml version="1.0" encoding="windows-1252"?>
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_8_4.xsd" version="ChemAxon file format v14.8.4, generated by v14.9.8.0">
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<propertyList>
<property dictRef="type" title="type">
<scalar>systematic</scalar>
</property>
</propertyList>
<atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9" elementType="C C C C C C O C R" sgroupRef="0 0 0 0 0 0 0 0 sg1" mrvPseudo="0 0 0 0 0 0 0 . 0" x2="1.3336791218280368 2.6673582436560745 2.6673582436560714 1.3336791218280346 0.0 1.3322676295501878E-15 1.333679121828039 4.26800012588501 1.3336791218280346" y2="2.310000000000002 1.5399999999999978 -2.220446049250313E-15 -0.77 1.9984014443252818E-15 1.5400000000000018 3.850000000000002 0.17599999904632568 -2.31"/>
<bondArray>
<bond id="b1" atomRefs2="a1 a2" order="2"/>
<bond id="b2" atomRefs2="a2 a3" order="1"/>
<bond id="b3" atomRefs2="a3 a4" order="2"/>
<bond id="b4" atomRefs2="a4 a5" order="1"/>
<bond id="b5" atomRefs2="a5 a6" order="2"/>
<bond id="b6" atomRefs2="a1 a6" order="1"/>
<bond id="b7" atomRefs2="a1 a7" order="1"/>
<bond id="b8" atomRefs2="a4 a9" order="1"/>
</bondArray>
<molecule id="sg1" role="SuperatomSgroup" title="SO3H" leftName="HO3S" molID="m2">
<atomArray atomID="a10 a11 a12 a13" elementType="S O O O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="4.576000051498413 5.346000051498413 5.346000051498414 3.036000051498413" y2="-2.4639999866485596 -1.1303208648205239 -3.797679108476595 -2.4639999866485596"/>
<bondArray>
<bond id="b9" atomRefs2="a11 a10" order="1"/>
<bond id="b10" atomRefs2="a10 a12" order="2"/>
<bond id="b11" atomRefs2="a10 a13" order="2"/>
</bondArray>
<AttachmentPointArray>
<attachmentPoint atom="a10" order="1" bond="b8"/>
</AttachmentPointArray>
</molecule>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

ChemAxon 2c555f5717

22-09-2014 07:40:41

Dear Bob,


   The only way I could do similar is adding a "[space]" as a pseudo label. We are going to discuss it more, and find possibilities, and decide what to do with the different cases, to get rid of hidden atoms.


Regards:
Balázs 

ChemAxon 4fa3cf533c

02-10-2014 12:45:39

Dear Bob,


We've found out how it is possible to draw an invisible atom like you mentioned.


1, Put down an atom


2, Place the cursor over the atom, and start typing something.


3, Press backspace until there is an invisible atom on canvas.


 


I've created a task in our issue tracking system, and we'll report back to you if it is done.


 


Have a nice day,


Tamas Fazekas-Vígh

User 870ab5b546

02-10-2014 13:57:53

Ahhh.... Brilliant detective work!