I had a problem with the 2D depiction of a large set of molecules using LICCS which uses jchempaint v 3.2 as teh base depictor. i ahev since reproduced the same problem directly with jchempaint which indicates the problem is not with the use of jchempaint by LICCS but a base problem with jchempaint. To exemplify the problem, I found a couple publicly available compounds that are not behaving properly. Here is my original post to the LICCS support group which again highlights the exact problem I am finding.
The depictions coming up from my smiles strings seem to have a large amount of overlapping in the structure images. I searched online for some public examples that fail in a similar fashion and I found a few. Here are two.
Example 1: CC1(C)(CC(=O)C(C(=O)C1)C(c2ccc(o2)N+[O-])C=3C(=O)CC(C)(C)CC=3(O)) (BAS 03161502 from Asinex collection)
See this link for example of non-overlaped structure on pubchem. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=3145896
Example 2: O=C2C1=CC=CC=C1C@H=C(O)\C(NC3=CC(C(C)=O)=CC=C3)=O)O2 (NSC 640982)
See this link for example of non-overlaped structure on pubchem. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=369251&loc=ec_rcs
The attached file is a jpg with the two depictions from LICCS (using jchempaint 3.2: reproduced when using jchempaint standalone) in them (left is example 2, right is example 1).