Yes. There is a confusion at the moment.
REFMAC LINK or LINKR record require link record that is absent in the
pdb.
If primary structure (sequence of amino acids/RNA/DNA and closeness in
3d of sugars) allow linking then links between residues used
automatically (TRANS/CIS/PTRANS/PCIS for peptides p or variations for
RNA/DNA and corresponding links for sugars). If residues are in
different chains then these links are not created automatically.
(There is an option to use them automatically but for incomplete model
the results may be misleading). In these cases a user can define links
explicitly between residues. For example:
LINK LYS A 27 TRP B
555 TRANS
Simple link record as it is in pdb does not allow to create chemical
description of polymers fully (for example if you write:
LINK C ASN B 729 N GLY B 741
It is not clear if bonds are single or double or is there any other
modification of residues before forming a covalent bond.
I hope this issue will be sorted out with pdb soon.
There is an option in refmac to create links if residues are close
each other but it may cause problem with incomplete models. When there
are deletions (gap between residues as in the above case) it is not
clear if it is because of incompleteness of the model or because of
actual deletions. With insertion codes situation is easier.
About LINK or LINKR: refmac tries to analyse the record and if it has
id then it assumes that it is refmac style link if it is not then it
is pdb style.
I hope it a little bit clarifies this confusing case.
regards
Garib
On 17 Aug 2009, at 10:17, Ian Tickle wrote:
>
> Tim, Garib,
>
> Sorry, maybe I'm missing something here but how does the user specify
> that (s)he wants a TRANS link between standard amino-acids (ASN-GLY)
> in
> this case? Isn't that the default? I always thought the answer was
> to
> add a LINK record for those two residues in the PDB file using the
> format specified in the PDB guide, e.g.
>
> LINK C ASN B 729 N GLY B 741
>
> (or just paste the LINKR record from the output PDB file and change
> LINKR to 'LINK ').
>
> But this raises an important issue. The PDB entries contain many
> examples of this, i.e. where there's a gap in the numbering but not in
> the sequence, and the PDB guide on the LINK record states:
>
> "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? 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:owner-
>> [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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