Ian,
Perhaps someone from one of the PDB deposition sites
could comment and verify my reading of this?
let me take the liberty. Your reading of PDB documentation is
absolutely correct. PDB format has got 3 types of links: SSBOND,
LINK and CISPEP. And indeed, residue numbers have no significance
in the PDB whatsoever. The connectivity is given by SEQRES and
by the order of residues in the coordinate section (which must
be identical to SEQRES). Where this order is insufficient to
describe (extra) connectivity, LINK etc. records are used.
LINKR was never in PDB standard and for this is not admissible.
I think (Garib will give an exhaustive explanation if he wishes)
Refmac uses them for purely technical purposes from long ago.
In the end of processing, they should become one of the PDB's
link records - either at depositor or PDB side, or be removed
if they are redundant.
I am sure Garib has reasons for having LINKR records in Refmac,
however confusing this may be. It is, indeed, not a very clean
practice to use self-invented additions to PDB format, but for
as long as they are used only locally there is no a terrible harm
in it as seems.
Best,
Eugene.
On Mon, 17 Aug 2009, 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:[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
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Stanford, CA 94305-5432
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FAX: (650) 736-1961
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