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: [log in to unmask] [mailto:[log in to unmask]]
>>
> On
>
>> Behalf Of Garib Murshudov
>> Sent: 16 August 2009 22:09
>> To: Tim Fenn
>> Cc: [log in to unmask]
>> 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 <[log in to unmask]>
>>
>>
>> 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
>> >
>>
>>
> 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
>> [log in to unmask]
>> 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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