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: [email protected] [mailto:owner-
[email protected]]
On
Behalf Of Garib Murshudov
Sent: 16 August 2009 22:09
To: Tim Fenn
Cc: [email protected]
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 <[email protected]>
On Fri, 14 Aug 2009 13:24:16 -0700
Jan Abendroth <[email protected]> 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
[email protected]
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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