Re: [modeller_usage] a question about loop refinement
To:
Subject: Re: [modeller_usage] a question about loop refinement
From: Modeller Caretaker <>
Date: Wed, 29 Feb 2012 16:13:29 -0800
Cc:
On 02/29/2012 05:28 AM, wrote:
I am a new user of the MODELLER package. I am using the modeller
package to refine a loop region of a X-ray crystal structure. I have
finished modelling 100 independent structures of that loop and in
order to pick out the "good" structures, I need to do cluster
analysis on these structures and then compare the representative
models from each cluster, am I right?
That would be one way to tackle the problem, yes, but there are various
ways you could do it (the ModLoop web server, for example, simply picks
the one model with the lowest energy; often visual inspection of an
ensemble is sufficient to identify the largest cluster).
My question is, could MODELLER package do this cluster analysis on
the loop structures I got?
While Modeller does include some basic clustering methods, you are
probably better off playing with specialist software for this to find
your favorite method.