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.
>
>
>
>
> --------------------------------------------------------------------------
> AstraZeneca UK Limited is a company incorporated in England and
> Wales with registered number: 03674842 and a registered office at 15
> Stanhope Gate, London W1K 1LN.
> Confidentiality Notice: This message is private and may contain
> confidential, proprietary and legally privileged information. If you
> have received this message in error, please notify us and remove it
> from your system and note that you must not copy, distribute or take
> any action in reliance on it. Any unauthorised use or disclosure of
> the contents of this message is not permitted and may be unlawful.
> Disclaimer: Email messages may be subject to delays, interception,
> non-delivery and unauthorised alterations. Therefore, information
> expressed in this message is not given or endorsed by AstraZeneca UK
> Limited unless otherwise notified by an authorised representative
> independent of this message. No contractual relationship is created
> by this message by any person unless specifically indicated by
> agreement in writing other than email.
> Monitoring: AstraZeneca UK Limited may monitor email traffic data
> and content for the purposes of the prevention and detection of
> crime, ensuring the security of our computer systems and checking
> Compliance with our Code of Conduct and Policies.
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Paul Emsley
> Sent: 08 June 2010 21:30
> To: [log in to unmask]
> 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 [[log in to unmask]] On Behalf Of Tim
> Gruene [[log in to unmask]]
> Sent: 08 June 2010 21:04
> To: [log in to unmask]
> 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
|