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:[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
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