But does it follow the PDB format for LINK records; it is a disaster if
the LINK read from the PDB have a different definition and information
content than LINK records output from REFMAC. At least LINKR is a
flagged non-standard record.
Eleanor
Garib Murshudov wrote:
In the latest, latest version refmac writes LINK instead of LINKR. It is
a temporary solution. We need a better solution and hopefully we will
have one soon
This version of refmac is available from:
www.ysbl.york.ac.uk/refmac/data/refmac_experimental/
regards
Garib
P.S. This version also has some low resolution refinement tools
On 9 Jun 2010, at 11:22, Debreczeni, Judit wrote:
Also, if you happen to use refmac for refinement: it rewrites LINK
records as LINKRs in the output pdb file -- and LINKR records are
unknown to Coot...
JED.
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-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
Paul Emsley
Sent: 08 June 2010 21:30
To: [email protected]
Subject: Re: [ccp4bb] JLigand Coot link
Briefly (and top-postingly),
Coot does not draw covalent bonds between non-tandem residues.
Coot will represent LINK records if they are in the PDB file.
Coot will respect the links generated by JLigand if you try to do sphere
refinement.
The Coot <--> JLigand internface will improve in the not too distant
future.
Paul.
________________________________________
From: CCP4 bulletin board [[email protected]] On Behalf Of Tim
Gruene [[email protected]]
Sent: 08 June 2010 21:04
To: [email protected]
Subject: Re: [ccp4bb] JLigand Coot link
Hi Sean,
do the ligand and the Thr belong to the same chain, and did you check
that the
distance between the bonding atoms is not beyond coot's cut-off?
Tim
On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote:
I have used JLigand v 0.2.1 to create a link between a Thr residues
and
a covalent adduct. The adduct refines well and shows up as a covalent
bond in PyMOL. However, when I'm in Coot there is no bond present
between the Thr OG1 and the ligand. I've loaded the Jligand link.lib
file that I created and the cif for the ligand itself into Coot. Any
ideas how to fix this?
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
