Template based cleaning

Hi,


I'm looking into cleaning structures according to a template and can't manage to change anything to my starting file.





The "full cleaning" (recalculating the atom coordinates) works fine but doesn't quite get the right orientation and I'm worried this could change over time.





I can't provide the structures I'm working with for confidentiality reason, but I'm attaching the template I use.


I'm actually not sure of the right file type to use (which might be the problem) but I've tried SDfile, MRV file & SMILES file with the same result.





Thanks in advance for any help on this.


Regards,





Geoffroy.

Hi,





What JChem version do you use ?





Best regards,


Zsolt

I indeed forgot that important information: 3.2.3





Regards,





Geoffroy.

...and indeed when using the latest version (3.2.5) it works much better!





But some structures appear to be completely scrambled while other very similar are fine... ?





Geoffroy.

Yes, some errors in template based clean have been fixed in JChem version 3.2.5 (see JChem changes: http://www.chemaxon.com/jchem/changes.html)





Can you send us an exaple structure, that became scrambled after clean, and the used template? If it is confidental, then please send it by mail, and you can also modify some parts of the structure.





Note: template structures have to be stored in formats that support storing coordinates (e.g. SDfile, MRV); SMILES can not be used. It is recommended to use ANY atoms in templates.


Example: http://www.chemaxon.com/jchem/examples/standardizer/index.html#tbclean





Best regards,


Zsolt

Thanks for these informations, they're very useful.





I'll send the "scrambled" structures in a separate email.





Regards,





Geoffroy.