Polymer Structure

Using Marvin Sketch 5.01 on a PPC Macintosh (G4 Powerbook) MacOSX 10.4.11.





Selecting a portion of the structure (leaving out the atoms that are not part of the polymer structure) and then grouping the atoms as suggested in the help documentation does not eliminate the unneeded atoms and replace with a star or leave a 'dangling' bond. The brackets are drawn but the 'extra' atoms are not eliminted.





The example I am working with is a simple condensation polymer - hydroxyls at both ends, with a water molecule eliminated to form the polymer.





Is this a bug or am I missing something.





By the way, this has become quite an amazing suite of programs.





Regards,





S. Kenendy

Hello,





The end groups of polymers are specified or unknown. Marvin uses * atoms to represent unknown end groups. When you draw a structure and create a polymer from it, Marvin automatically changes the terminal carbons to * atoms.


When you draw a structure where the end groups are specified (for example hydroxyls at both ends in your example instead of carbons), Marvin expects that you are drawing a polymer with specified end groups and doesn't replace the end group with * atoms.





First change the specified end groups to carbons in your structure, so the star atoms will be automatically added when creating polymer from the structure.





I hope this helps.





Regards,


Erika.

Thanks Erica,





That worked. It wasn't clear from the help file that the 'end atoms' to be replaced needed to be carbons.





Steve