Sketcher problem

From: reyhan muhammad
Date: 21 October 2011 02:08

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

 

 

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From: Debreczeni, Judit

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.

 

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From: Paul Emsley

I agree with that.

Just to say that Coot (seeing as you mentioned it), as yet, does not deal with cross-compound torsion manipulation.  Sorry about that. 

Having said that, as Judit suggests, it is not obvious that you need it.

Paul.

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From: reyhan muhammad

I just tried your suggestion, and it seems to work satisfactorily.
Great. Many thanks.

best,
reyhan