Re: [modeller_usage] breaking the chain

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 05/29/2012 06:58 AM, M wrote:
> I don't want to model one fragment of a protein. I want to achieve
> this by using the "\" sign in the alignment, but I'm not sure how the
> pir file should look after insertion of the "\" sign. Should it look
> like this:

You're close, but you need to make two changes:

1. It's the '/' sign, not the '\'.

2. Since a chain break denotes a break *between* two residues, it has 
zero width. It doesn't make sense to align a chain break with a 'real' 
residue; you need to align it with either another chain break or a gap. 
So in this case you probably want to add a gap to your template:

>P1;template
structureX: (...)
ABCDEFGH-JKLMNOPQRSTUVWXYZ*

>P1;target
sequence: (...)
ABCDEFGH/-------QRSTUVWXYZ*

Note also that your example alignments are not valid PIR format; each 
sequence must start with >P1; as above, not <P1 or <P2.

	Ben Webb, Modeller Caretaker
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