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Re: [ccp4bb] JLigand Coot link |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: JLigand Coot link From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2010-06-09 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. >> >> >> >> >> -------------------------------------------------------------------------- >> >> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Paul Emsley >> Sent: 08 June 2010 21:30 >> To: CCP4BB@JISCMAIL.AC.UK >> 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 [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim >> Gruene [tg@SHELX.UNI-AC.GWDG.DE] >> Sent: 08 June 2010 21:04 >> To: CCP4BB@JISCMAIL.AC.UK >> 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 CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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