This solved my problem. I had indeed rebuilt that part of the molecule just before and though there was a continuity in numbers, the actual location of some of the residues were placed at the end of the file. I changed that and it solved the problem.
Meanwhile I came across an old email from Warren de Lano that advised to use the commands "set retain_order" and then "rebuild" I've tried that also and that appears to work too.
On 27/07/12, "Noinaj, Nicholas (NIH/NIDDK) [F]" <firstname.lastname@example.org> wrote:
hi, not sure if anyone has replied, but one thing you can check is to verify that these segments are listed in proper order in the actual pdb file. i know that, for example, if residues 5-10 are listed before residues 1-4 in the pdb, this won't have any affect on refinement or displaying them in stick, but it does make the cartoons disjoint as you describe.
i am happy to take a quick look if sharing the pdb coordinates is possible at this point. hope something here helps...good luck!
From: Sebastien Vachieri [email@example.com]
Sent: Friday, July 27, 2012 7:15 AM
Subject: [PyMOL] Cartoon gap problem
When I try to display my protein with cartoon I have gaps at several positions but this does not occur if lines, sticks or ribbons representations are used instead of cartoon. The residues involved do not have insertion codes or anything special, eg the cartoon tube stops at Asn 161 CA and restarts at Tyr 162 CA but no atoms are missing in the pdb files.
Does anybody know a way around this?