On Mon, Jun 27, 2016, Prayagraj Fandilolu wrote:
> trajin md.crd
> average 2180-2500.pdb pdb start 2180 stop 2500 .1-66
> The pdb which I get after processing shows much more overlapped and
> distorted structure.
Calculating an average structure without first doing some sort of rms
fit (to remove overall translation and rotational motion) will always
lead to bad behavior.
> What input should I design so as to get clear average structures with no
> distortions?
You will never get average structures with "no" distortions: an average
structure is always distorted to some extent. Many people look for the
snapshot that is closest to the average, and use that for further analysis.
...dac
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Received on Mon Jun 27 2016 - 05:30:03 PDT
