On Fri, 14 Aug 2009 13:24:16 -0700
Jan Abendroth <[log in to unmask]> wrote:
> 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?
>
take a look at the data_link_list loop in mon_lib_list.cif (there may
be an easier way to view this info):
TRANS . . peptide . . peptide
default-peptide-link
PTRANS . . peptide PRO . .
default-peptide-link_pro
NMTRANS . . peptide PRO . .
default-peptide-link_cn
CIS . . peptide . . peptide
cis-peptide-link
PCIS . . peptide PRO . .
cis-peptide-link_pro
NMCIS . . peptide PRO . .
cis-peptide-link_cn
so you probably want TRANS.
HTH,
Tim
--
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Tim Fenn
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Stanford University, School of Medicine
James H. Clark Center
318 Campus Drive, Room E300
Stanford, CA 94305-5432
Phone: (650) 736-1714
FAX: (650) 736-1961
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