Hi Jared,
Thank you so much for your help - this was driving me crazy for hours! I used your first solution to keep everything as a single chain, and it worked perfectly. Again, many thanks for your help.
Nick.

> From: Jared.Sampson@nyumc.org
> To: wimock@hotmail.com
> CC: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Pymol insertion code
> Date: Thu, 20 Mar 2014 17:26:21 +0000
>
> Sorry - one quick correction to my previous email:
>
> On Mar 20, 2014, at 10:50 AM, Sampson, Jared <Jared.Sampson@nyumc.org> wrote:
>
> > If you don’t need the cartoon representation to be continuous (e.g. if you’re zooming in on a different section of the protein you can replace the 3rd line with:
> >
> > alter prodomain, chain=“P”
> >
> > to split off the prodomain into a separate chain. In this case, the sequence will be numbered as in the PDB, only without the insertion code.
>
> The numbering will be exactly as in the PDB, only the chain ID will differ.
>
> Cheers,
> Jared
>
>
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