[Chimera-users] axis-axis distance definition

Eric Pettersen pett at cgl.ucsf.edu
Thu Aug 13 16:53:02 PDT 2015


Yes, it’s the shortest distance between the axes, but not treating them as infinite.  There is support in the code for treating them as infinite, but currently no way to invoke that support without using a Python script.

—Eric

> On Aug 13, 2015, at 4:46 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Actually never mind, it seems to be the minimum distance between the axes as displayed. The minimum distance between infinite axes might also be a useful measurement when looking at conformational changes, as it is not dependent upon the axis length (e.g. if helices are of slightly different lengths between two otherwise homologous structures).
> 
> Oliver.
> 
> 
>> On Aug 13, 2015, at 7:38 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>> Quick question - how is the distance between two axes (as reported by Axes/Planes/Centroids) calculated?
>> 
>> Is it the minimum distance between two axes (I guess yes, because it does not seem to match the center to center distance)? And does it assume the axes are of infinite length, and calculate the displacement required for them to intersect, or does it measure the minimum distance between the axes with the length and end positions as displayed?
>> 
>> Cheers,
>> Oliver.
> 
> 
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