[Chimera-users] Fwd: Re: Bug (?) with EnsembleCluster

[Elaine Meng]

On Jan 16, 2008, at 10:35 AM, Francesco Pietra wrote:

>
>> If you look at just the top tiny line in the RMSD map (frame 1 vs.
>> all the others) it contains that information in terms of color,
>
> I may have better waited until I understand what you suggest. It is  
> the hope to
> further clarify my things that urges me to ask for that explained  
> with other
> words. I don't understand where to look at.
>
Here is the RMSD map, which is a 80 x 80 grid comparing the 80 frames  
in 1plx.pdb:

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RMSD vs. time using frame 1 as the reference is the top 1 x 80 of the  
grid:

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you see that comparison to self (grid position 1,1) is white (0  
RMSD), comparison to frame 2 (grid position 1,2) is black (higher  
RMSD), then there are several frames with low RMSD compared to frame  
1, then ending with several frames with high RMSD compared to frame 1.

To use frame 2 as the reference instead of frame 1, you would use  
next-to-top 1 x 80 of the grid (positions 2,N), etc.

Elaine