Unfortunately, this is not something PyMOL can do at present, and we were not able to come up with a workaround previously.
 
In short, the code needs to be modified at a fundamental level, but the cartoon generator in PyMOL is about as bad as it gets: deeply nested code, 1-2 letter variables names, fragile pointers, and almost all of it in one massive ~2,000 line C subroutine.  RepCartoon.c is one of those skeleton demons in the closet that must eventually be challenged but will not be easily defeated...apologies.

From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of jkulpiii@netscape.net
Sent: Wednesday, March 07, 2007 11:33 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] cyclic structures

This question has appeared a few times in the mailing list yet I could not find any answer (maybe I missed it).

http://sourceforge.net/mailarchive/message.php?msg_id=10556819
http://sourceforge.net/mailarchive/message.php?msg_id=36990895

Basically, in cyclic structures there is a discontinuity at the last residue to the first residue when displaying the cartoon representation.  How do we make a cyclic cartoon representation?

Cheers,
John Kulp
NRL

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