AMBER Archive (2003)

Subject: AMBER: Simulation of small protein (MD Display tips)

From: Chris Moth (Chris.Moth_at_vanderbilt.edu)
Date: Fri Oct 24 2003 - 13:56:38 CDT

At 01:27 PM 10/23/2003 -0400, you wrote:

>Dear Carlos,
>its the villin headpiece which was described as a thermostable, fast folding
>alpha-helical subdomain. I also looked at the trajectory with mddisplay:
>at the beginning of the movie the structure seems a bit more open, but its
>hard to tell since its just a bunch of wobbling atoms.

Some MDDisplay tips which might help:

You might try hiding the side chains:

<0> (zero - black on the <c>olor palette)
@SC<ENTER>

You can filter out higher frequency motions with <F>ilter and the entering,
6 (or so)<ENTER>

Finally, the "Static" menu button will let you see the first or average
frame in grey, on which your dynamic structure will be superimposed

The above are documented a bit on the '?' panel

Thanks again for trying MD Display!

Chris
http://www.structbio.vanderbilt.edu/~cmoth/mddisplay

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