Sorry for the double post. Forgot to change the subject line in the last and also pasted the wrong link... Anyway, check for discontinuous SEGIDs and here is the old thread.

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07683.html

Eric

On Jul 23, 2012 6:32 AM, "Eric Larson" <larsonet@gmail.com> wrote:
>
> Hi Malai,
>
> Do you happen to have values in the SEGID column of your pdb file?  If so, simply delete them. Not sure if pymol still behaves the same but this used to cause problems with cartoon rendering.  See this old post:
>
> http://www.google.com/search?hl=en&redir_esc=&client=ms-android-verizon&source=android-launcher-widget&v=133247963&qsubts=1343038842699&action=devloc&q=segid+pdb+file&v=133247963
>
> Good luck,
>
> Eric Larson
> Boehringer Ingelheim
> Ridgefield,  CT
>
> > Date: Sat, 21 Jul 2012 04:09:13 +0800
> > From: Malai <winterhot82@gmail.com>
> > Subject: [PyMOL] Very strange problem
> > To: pymol-users@lists.sourceforge.net
> > Message-ID:
> >         <CANDSGMEh4of1NMn1VGZ=CS_mzwgiVFOgpvC16VbJQC_eAN2GHg@mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi Pymol users,
> >
> > I am using Pymol 1.5.0.0. I tried to cartoon for the complex but Pymol can
> > not assign the cartoon for some parts of complex. When I use
> > some commercial visualizer like MOE and Discovery Studio. It works well.
> > Could you help me what is the problem in the structure or pymol?
> >
> > Many thanks in advance.
> >
> > With regards,
> > Malai
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Fri, 20 Jul 2012 17:44:35 -0500
> > From: Jason Vertrees <jason.vertrees@schrodinger.com>
> > Subject: Re: [PyMOL] Very strange problem
> > To: Malai <winterhot82@gmail.com>
> > Cc: pymol-users@lists.sourceforge.net
> > Message-ID:
> >         <CAAx+4zdrYJWmK3SBpQWMvBCUhEZ5szACpzNemps7S5CA708qvw@mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi Malai,
> >
> > What structure? Can we see it? (Feel free to send it to me if you can share it.)
> >
> > Cheers,
> >
> > -- Jason
> >
> > On Fri, Jul 20, 2012 at 3:09 PM, Malai <winterhot82@gmail.com> wrote:
> > > Hi Pymol users,
> > >
> > > I am using Pymol 1.5.0.0. I tried to cartoon for the complex but Pymol can
> > > not assign the cartoon for some parts of complex. When I use some commercial
> > > visualizer like MOE and Discovery Studio. It works well. Could you help me
> > > what is the problem in the structure or pymol?
> > >
> > > Many thanks in advance.
> > >
> > > With regards,
> > > Malai
> > >
> > > ------------------------------------------------------------------------------
> > > Live Security Virtual Conference
> > > Exclusive live event will cover all the ways today's security and
> > > threat landscape has changed and how IT managers can respond. Discussions
> > > will include endpoint security, mobile security and the latest in malware
> > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > > _______________________________________________
> > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schr?dinger, LLC
> >
> > (e) Jason.Vertrees@schrodinger.com
> > (o) +1 (603) 374-7120
> >
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Sat, 21 Jul 2012 08:07:14 +0200
> > From: Tsjerk Wassenaar <tsjerkw@gmail.com>
> > Subject: Re: [PyMOL] Very strange problem
> > To: Jason Vertrees <jason.vertrees@schrodinger.com>
> > Cc: Malai <winterhot82@gmail.com>, pymol-users@lists.sourceforge.net
> > Message-ID:
> >         <CABzE1SiMBzPfSi3pkw7Wn_MR4QfTViZhDWPKsnR9kSyEyhFSqA@mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Malai,
> >
> > Check whether all residues have unique identifiers (residue id + chain id).
> > I often see this happen for multiple chains with no or identical
> > identifiers, in which different residues share the same number.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Jul 21, 2012 12:46 AM, "Jason Vertrees" <jason.vertrees@schrodinger.com>
> > wrote:
> >
> > Hi Malai,
> >
> > What structure? Can we see it? (Feel free to send it to me if you can share
> > it.)
> >
> > Cheers,
> >
> > -- Jason
> >
> > On Fri, Jul 20, 2012 at 3:09 PM, Malai <winterhot82@gmail.com> wrote: > Hi
> > Pymol users, > > I am us...
> > >
> > ------------------------------------------------------------------------------
> > > Live Security Virtual Conference
> > > Exclusive live event will cover all the ways today's security and
> > > threat landscape has changed and how IT managers can respond. Discussions
> > > will include endpoint security, mobile security and the latest in malware
> > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > > _______________________________________________
> > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schr?dinger, LLC
> >
> > (e) Jason.Vertrees@schrodinger.com
> > (o) +1 (603) 374-7120
> >
> > ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> > -------------- next part --------------
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> > ------------------------------