Re: [PyMOL] Pymol insertion code

[Wimock]

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.samp...@nyumc.org
 To: wim...@hotmail.com
 CC: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Pymol insertion code
 Date: Thu, 20 Mar 2014 17:26:21 +
 
 Sorry - one quick correction to my previous email:
 
 On Mar 20, 2014, at 10:50 AM, Sampson, Jared jared.samp...@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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[PyMOL] Pymol insertion code

[Wimock]

Hi,
I'm new to Pymol and am looking at the structure of pepsinogen (PDB: 3psg). 
This protein contains a 44 residue prodomain, which the pdb file says is 
assigned an insertion code 'P' and labelled 1 - 44. This prodomain is cleaved 
to yield pepsin (5pep), whose sequence is labelled 1 - 326. I gather Pymol 
should be able to see these as separate parts of the sequence, but it instead 
seems to interleave the sequences - I don't know if this affects the structure 
or not? Other programs (Chimera) show the sequence as it should be 
(P1-44...1-326).
Is there a way to have the sequence parts recognised in the sequence viewer? 
This would make it much easier for me to manipulate these sections. Please let 
me know if I haven't been clear.
Thanks,Nick.  --
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