Re: Generation of average trajectory

From: Roman Petrenko (
Date: Mon Oct 12 2009 - 21:02:03 CDT

could you please explain how you superimposed structures from
trajectories and colored them according to rmsf. I am doing it using
many scripts. Just wondering if there is a simpler way to do it.

On Mon, Oct 12, 2009 at 6:06 AM, Nicholas M Glykos <> wrote:
>> I have simulated 50 simulation trajectories of a protein unfolding
>> starting from same structure, but with different seed numbers. Then I
>> have clustered them according to their RMSD and Rg behavior. So for each
>> cluster, I wish to look at the average trajectory, which can be looked
>> as representative trajectory of that respective cluster. If I just
>> average out the coordinates per timeframe, then will it be a realistic
>> average trajectory representative of that set of 10 simulations? I am
>> going through the literature, but I am stuck and am not able to find a
>> better solution. If there is any other better and correct way of
>> generating an average trajectory, please suggest.
> I'm not sure what this 'average trajectory' may be. If you want an image
> showing the amount of mobility encompassed by a cluster, ie. something
> like this figure
> then, all you need is a set of representative (superimposed) PDB files
> corresponding to trajectory frames that belong to a given cluster (and,
> possibly, colored according to atomic fluctuations as calculated from
> the cluster).
> Apologies if this is not what you had in mind.
> --
>          Dr Nicholas M. Glykos, Department of Molecular Biology
>     and Genetics, Democritus University of Thrace, University Campus,
>  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
>    Ext.77620, Tel (lab) +302551030615,

Roman Petrenko
Physics Department
University of Cincinnati

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