On Mon, Sep 20, 2004 at 03:57:16PM +0100, John Simms wrote: > I have a small problem. I work on GPCRs and would like to use some electron > crystallography data. However, the data given are distances between the > centres of transmembrane alpha helices rather than a specific atom eg CA. > Does anyone know how I would specify the centre of a helix when using > distance restraints?.

You can't specify the 'centre' of a helix, but you can define pseudoatoms which are gravity centres of two or more real atoms, and you can then put distance restraints onto those pseudoatoms. (Probably the centre of some CAs around the middle of the helix sequence would approximate the helix centre fairly well, depending on where Modeller decides to put your helices, of course.)

See also: http://salilab.org/modeller/manual/node100.html http://salilab.org/modeller/archive.html

Ben Webb, Modeller Caretaker