Hi,
"The LINK records specify connectivity between residues *that is not
implied
by the primary structure*." (my emphasis).
My reading of this is that it's the primary structure (i.e. the SEQRES
records) that specify that the residues are contiguous, *not* the
residue numbering. Perhaps someone from one of the PDB deposition sites
could comment and verify my reading of this?
Ian is correct. In the PDB, LINK records are only really used to
describe bonds that are not immediately obvious based on residue name.
For example, Link records could be used to describe coordinate bonds
between metal and amino acids, connections between modified residues and
standard residues, or even glycosidic bonds between sugars. Standard
connectivity is assumed between all standard polymer chains based on the
sequence (SEQRES) and not residue numbering as has been pointed out. As
long as two residues are contiguous inside a SEQRES record, it is
assumed they have standard connections and therefore no LINK records are
necessary (as far as the PDB is concerned) for such residues.
best regards-
Jawahar Swaminathan
PDB Depositions
Protein Databank in Europe (PDBe)
http://www.ebi.ac.uk/pdbe
If this is the case then
Refmac is ignoring a perfectly valid PDB format, and requiring that the
user supplies a non-agreed format! - but of course I could be wrong in
my interpretation (in which case of course I withdraw from the
argument!). But if I'm right then it seems to me that refinement
programs should at the very minimum be able to treat completely valid
PDB entries correctly, and not require the user to make non-standard
changes.
Cheers
-- Ian
-----Original Message-----
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Garib Murshudov
Sent: 16 August 2009 22:09
To: Tim Fenn
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] LINKR in refmac
Tim is right. The link you want is TRANS. And if you want link between
alternative position then you need to add alt codes before residue
names.
Llink ids must be defined in the dictionary. There are definitions for
standard links in the dictionary: $CLIBD_MON/list/mon_lib_list.cif.
For templates how to use various forms of links please have a look:
http://www.ysbl.york.ac.uk/refmac/data/template_link.txt
If you experience further difficulties please let me know and I will
try
to sort this out.
regards
Garib
2009/8/14 Tim Fenn <f...@stanford.edu>
On Fri, 14 Aug 2009 13:24:16 -0700
Jan Abendroth <jan.abendr...@gmail.com> 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
>
123456789012345678901234567890123456789012345678901234567890123456789012
34
567890
> 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
--
---------------------------------------------------------
Tim Fenn
f...@stanford.edu
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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