Thanks Nick,
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.
Thanks again,
Seb
On 27/07/12, "Noinaj, Nicholas (NIH/NIDDK) [F]" <noin...@niddk.nih.gov> 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!
>
>
>
>
> Cheers,
> Nick
>
>
>
>
>
>
> ________________________________________
> From: Sebastien Vachieri [svac...@nimr.mrc.ac.uk]
> Sent: Friday, July 27, 2012 7:15 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Cartoon gap problem
>
> Hi All,
>
> 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?
>
> Cheers,
>
> Seb
>
>
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