Dear Phil,

Sorry for the delay, I am only just back from somewhat extensive travels.

On 01/11/10 12:26, Phil Evans wrote:
If I "colour by chain" (my preferred option), metal ions disappear

Thanks for the notification of this bug.  It is fixed now, rev 3245.

also is there any way of refining a zone around a metal ion without the sidechains 
vanishing into the metal density? I know the refine-by-sphere ("R") option 
works better, but then I have no control over what I'm refining


Sphere refine is simply a thin layer around the refine-residues function which takes a list of residue specs - that gives you enough control, I hope. (You can also trivially change the "radius" in sphere refine.)

Paul.

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