Re: [AMBER] clustering analysis changes my coordinates

From: Geoffrey Wood <gwood.MIT.EDU>
Date: Sat, 24 Jul 2010 21:06:52 -0400

Thanks. That was the use that I wanted to make of it. It is fairly straight forward to change the code... but I guess you need to add the interface as well.


On Jul 23, 2010, at 11:51 AM, Thomas Cheatham III wrote:

>> 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 Sat Jul 24 2010 - 18:30:03 PDT
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