There are differences between the LINK pdb definition and that in REFMAC -
hence the different name LINK and LINKR
LINKR allows you to do this: ie cross reference to a dictionary link which
is much more informative than a simple LINK record which can only define a
link distance.
However for reasons I do not know this addition has never been adopted as
standard PDB information so there is confusion between different programs..
Eleanor.
Definition of LINK with LINKR part in red.
The LINK records specify connectivity between residues that is not implied
by the primary structure. Connectivity is expressed in terms of the atom
names. This record supplements information given in CONECT records and is
provided here for convenience in searching.
Record Format
COLUMNSDATA TYPE FIELD DEFINITION
1 - 6Record name LINK
13 - 16Atomname1 Atom name.
17 Character altLoc1 Alternate location indicator.
18 - 20Residue nameresName1Residue name.
22 Character chainID1Chain identifier.
23 - 26Integer resSeq1 Residue sequence number.
27 AChar iCode1 Insertion code.
43 - 46Atomname2 Atom name.
47 Character altLoc2 Alternate location indicator.
48 - 50Residue nameresName2Residue name.
52 Character chainID2Chain identifier.
53 - 56Integer resSeq2 Residue sequence number.
57 AChar iCode2 Insertion code.
60 - 65SymOP sym1Symmetry operator for 1st atom.
67 - 72SymOP sym2Symmetry operator for 2nd atom.
73 - 80LinkID linkid Cross-reference to LINK
definition in CCP4 libraries
On 28 May 2014 16:10, herman.schreu...@sanofi.com wrote:
Dear Remie,
For reasons that probably only Garib understands, Refmac still uses LINKR
instead of LINK to link atoms. However (at least for Refmac) both LINK and
LINKR should work.
After a lot of complaining in the past (also from my side), the handling
of carbohydrates in Refmac is ok. I just did some tests with N-linked
carbohydrates (NAG, MAN): after using the Make Link option in coot and
saving the file, there were regular LINK records, created by coot. After
running refmac from within coot and saving the files, the LINK records were
converted (perverted?) to LINKR records. However, they did not disappear
and after restarting coot and loading the file again, they were still
there. Also my version of pymol recognizes both LINK and LINKR records,
since the connections are shown when I load the files before and after
running refmac.
Some suggestions: check that you are using recent versions of coot, refmac
and pymol. Older versions may have problems. I don't know how you construct
your carbohydrates, but if you get the monomers, you have to delete an
oxygen atom in the link (in my case the O1 atom). Make also sure that your
starting geometry is acceptable. Just doing a real space refinement usually
works well, but sometimes the carbohydrate crashes into the protein density
and you will have to manually fit the sugar as good as possible. Some of
the older files in the PDB may have distorted carbohydrates, so here it is
probably best to build the carbohydrates again from scratch (get monomer,
delete linking oxygen) etc.
Good luck!
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Remie Fawaz-Touma
Gesendet: Mittwoch, 28. Mai 2014 16:13
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Refmac5
Hello everyone,
When I refine in CCP4 a structure with Glc units attached every few of
them as a ligand and there are several of them in the same file, I start
off with a PDB that shows the LINK records between the GLC units as LINKR
because I add the links by Extensions Modelling Make Link (2 atoms)
in COOT.
What does LINKR mean? why not just LINK?
More importantly, when I refine, the output PDB file does not contain the
LINK records, why do they go away? and in PyMol I see only GLC that are
close enough to make a covalent bond stay connected, the others become
detached, in CCP4 they all show detached, but if I do a real space
refinement for those sugars of the same ligand in the output file, they
come close together and attached?
Any suggestions?
Thank you very much in advance.
Remie
