Preserving a structure layout between saves and loads

Hi,

I've recently been using MarvinSketch to draw some small biological molecules, mostly similar analogues. Much to my frustration however, despite the fact that I'm laying out each of the molecules in a very specific manner for reasons of space and readability, I find that Marvin is doing what appears to be a structure cleanup between each save and load.

Its also expanding all my collapsed groups which is frustrating when I'm trying to change specific amino acids.

I'm running it on OSX 10.6.3, MarvinSketch is 5.3.02 and I'm saving my files in the ChemAxon Extended SMILES format, which appears to be the default when saving a file for the first time.

What can I do about this?

 

Thanks.

Hi,

SMILES format cannot store atomic coordinates and S-group information, this is why your structures are automatically cleaned and ungrouped. Use a richer format, e.g. MRV.

Best regards,

Akos