chirality depiction question?

Hello,





As part of a new build test, I have processed some molecules that contain chiral carbon atoms between two JChem tables. As expected I find that the chirality is propagated correctly between tables and that the SMILES underneath are consistently migrated...However a point regarding the depiction...it appears that at least one of the projected bonds appears to lose (visual) information on processing between tables (at least the depiction suggests this), this does not matter as much if the chiral C atom is part of a ring system, however if it is not then it appears the structure could be ambigiously interpreted by the viewer?





Example1: Cl[C@]1(Br)CCCC1=O


The bond projecting back is not visible in MarvinSketch/View even though the SMILES defines that it has to be projected back, the viewer knows this has to be the case visually...In the initial table where molecule first created all chiral bonds were fully defined...and the SMILES in each table are identical...





Example2:


C\C(C1CCCCC1)=C\C=C/[C@@](C)(F)Br


The bond projecting back is not visible in MarvinSketch/View leading to ambigious interpretation of what the actual absolute stereochemistry is?


(The SMILES and thus queries are fine so maybe the "issue" is purely in MarvinSketch/View handle of chiral carbon). In the initial table where molecule first created all chiral bonds were fully defined...and the SMILES in each table are identical...





I have not specified any standardization w.r.t to either table that relates to chirality and so assume it occurs naturally...I say again the data underneath is consistent but the visulaisation of this data appears not to be...Any comments gratefully received on this observation?





Cheers,


Daniel.

Hi Daniel,





Which Marvin version are you using? I checked the two smiles in Marvin 4.0.6, and I could see the wedge bond in both.





Szabolcs

I am using this build for everything:





TEST_2006_05_17





So that is JCMAN, JSP and JC_INSERT, the lot and that is what I see...


Not sure how this build relates to Marvin version?








Cheers,


Daniel.

I see. That one uses a previous Marvin alpha release, specifically Marvin 4.1.0alpha15. Our most recent alpha (alpha20) also displays both smiles correctly, so this bug has been fixed since.





Thank you for keeping a watchful eye.





Best regards,


Szabolcs

OK, so presumably if I upgrade to 3.1.7 this retro issue will be fixed?

Yes. JChem 3.1.7 contains Marvin 4.0.6., which was also fine with the smiles strings. (As all stable releases, I believe.)





The only thing is that from the JChem alpha TEST_2006_05_17 to 3.1.7 it would be rather a downgrade than an upgrade. For an upgrade to a stable version, you would have to wait for JChem 3.2.





Szabolcs