RE: [ccp4bb]: Refmac makes proteingaps that I don't want

[Mathias Färnegårdh <mathias.farnegardh@karobio.se>]

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I got it sorted out - I tried to define the peptide LINK explicitly using the 'edit restraints in pdb' unfortunately that gives a wrong format of the link statement and refmac doen't really complain about that it just ignores it. Thanks to Robert Steiner I got one link statement with the correct format. 

The edit restraints format on top and the correct format below.
LINK             GLY A 369                      GLY A 372                   TRANS
LINK             GLY A 369                     GLY A 372                TRANS

/mathias

-----Original Message-----
From: Eleanor J. Dodson [mailto:ccp4@ysbl.york.ac.uk] 
Sent: den 24 april 2003 12:02
To: Mathias Färnegårdh
Cc: ccp4bb@dl.ac.uk
Subject: Re: [ccp4bb]: Refmac makes proteingaps that I don't want


  This makes life SO complicated that I would simply renumber the 
residues to make a continuous chain.
You can do this in the GUI under coordinate utilities - renumber chain 
option

(But use a pencil and paper first to work out what you want to renumber!)

Eleanor

Mathias Färnegårdh wrote:
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Dear Refmac users
> 
> I have a protein where we removed (on DNA level) some residues in a 
> loop which means that some residues are missing in the crystallized protein. I haven't figured out how to persuade refmac to realize that for instance residue 34 and 36 should be directly connected. Refmac interprets the gap in sequence numbers as a peptide bond gap although I've built them with nice peptide bonds in O before kicking them into refmac - some asssitance would be greatly appreciated.
> 
> /mathias
> 
> 
>