Re: [AMBER] clustering analysis changes my coordinates

From: Thomas Cheatham III <>
Date: Fri, 23 Jul 2010 09:51:43 -0600 (Mountain Daylight Time)

> So I looked through the code and it doesn't matter if you are using the
> rms or dme metric, but it seems to realign to the centroid after every
> pass (in the means algorithm anyway) not just at the end of the

We're cleaning up a version that does this, i.e. like a "nofit" on the RMS
command, which is useful for example for fitting on the protein core but
then clustering the loops without another (global) RMS fit over those
atoms... I'll push to accelerate the time table on this by pushing Dr.
Jianyin Shao in my group. --tec3

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Received on Fri Jul 23 2010 - 09:00:03 PDT
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