Oops. The measurement isn't honoring the relative motion of the models -- the values you see are for the original coordinates of the models. I've just committed a fix so that it does consider the relative positioning of the models when computing the angle/distance values. It will be in tonight's build and you should be able to get it tomorrow (www.cgl.ucsf.edu/chimera -- follow the "Daily Builds" link). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 7, 2008, at 2:49 PM, Giovanni Cardone wrote:

Hi everybody, I have a doubt about my proper using the tool Axes for measuring angle between helices. After aligning two model and generating the axes corresponding to the helices of interest, I select them in the 'Structure Measurements' dialog windows. As you can see from a snapshot, they look properly selected. They are almost overlapping, but in the Reply Log I get the following info:

col_best_001.pdb helix 10/col_best_005.pdb helix 2 crossing angle: 36.9 degrees, distance: 15.3 angstroms

Beside the value of the angle seeming to me too high, shouldn't the distance between the helices be within few angs (at least according to how I interpret the documentation)? Probably I am missing something.

Thanks in advance, Giovanni Cardone

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