Hi all,
I am hitting the wall on this one: A disordered loop has been replaced with
a short linker, which now is visible in the density. To be consistent, I
maintain the original residue numbering and get a gap of residue numbers
between the last original residue and the first residue of the loop. Refmac
thinks that these residues are not supposed to be linked, and pulls them
apart.
How can I tell refmac to maintain the peptide link?
Here is what I tried - the numbers above just for orientation
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
LINKR C ASN B 729 N GLY B 741
ASN-GLY
refmac comments in the log file ... however, still pulls the residues apart.
WARNING : description of link:ASN-GLY is not in the dictionary
link will be created with bond_lenth = 1.260
So, in my understanding it comes down to the question:
how is a peptide bond referenced to in the dictionary?
Any ideas are welcome!
Thanks!
Jan
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Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island, WA, USA
work: JAbendroth_at_decode.com
home: Jan.Abendroth_at_gmail.com
