IIUC, you would like to keep the distance between the ring plane and the Ru fixed and allow the ring to rotate freely.
I would define bond length restraints between each of the ring atoms and Ru (I suspect that these distances will be the same for each atom pair) -- the ring will rotate freely if no torsion or angle restraints are defined between the ring and the metal, i.e. no need to define the imaginary axis. (Bond, angle and planar restraints for the ring itself will still have to be defined to keep it in a decent shape, needless to say.) I would personally edit the restraints file by hand, but you might wish to try JLigand -- the tool of choice for metal containing ligands. From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of reyhan muhammad Sent: 21 October 2011 02:09 To: [email protected] Subject: [ccp4bb] Sketcher problem Greetings everyone, This is my first post here. I am trying to build a compound on sketcher. The molecule is ruthenium-centered, with 4 coordination ligands around the ruthenium (picture is attached). Three of the ligands are definite atoms, but the fourth one is a benzene derivative. My problem is I want this benzene ring to be able to spin (at least on coot) around to the 'hypothetical' axis between ruthenium atom and the centre of the benzene ring. While the axis for the other three ligands can be easily defined on the library file, I dont know how to set a description for the benzene ring as there is no real atom in the centre of the benzene that can be used to define the axis. Please advise me on this matter. Thanks a lot Best regards, Reyhan -------------------------------------------------------------------------- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. 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.
