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:[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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