[Molvis-list] FirstGlance /Jmol: A few observations

[Gale Rhodes]

Hi, Eric!

Earlier, Gale Rhodes wrote, concerning model validation tools in  
visualization software,

>>  With the same command (color by B-factor),
>> NMR models are colored by how much each atom's position varies across
>> the ensemble of models (rmsd from the average position), also a
>> quality indicator. (The same PDB file column that contains B-factors
>> for x-ray models contains rmsds for NMR models, and contains
>> uncertainty indicators for homology models, so one command fits all.)

On Feb 17, 2006, at 2:00 PM, Eric Martz wrote

> I do not find this to be true for ensembles of NMR models, e.g.  
> 2BBN. However, it may be generally true for minimized average  
> models, e.g. 2BBM -- but these are often not published in the PDB.  
> Perhaps you are "thinking DeepView", which may have such a color  
> scheme calculation built-in?

You are correct. RMSDs are present in B-factor column only in the  
increasingly rare (and ill-advised) minimized averaged models. But  
DeepView allows coloring by RMSD for individual members of the  
ensemble, or coloring the whole ensemble by the overall RMSD.

For coloring individual members by RMSD from the first model, hold  
down shift (to affect all models) and use the command Color:RMS.

For coloring the entire ensemble by overall RMSD, use the command  
Fit:Set Layer Std Deviation into B Factors. Then the same residues in  
each model will be colored identically: according to overall RMSDs  
for the ensemble. This commands rewrites the contents of the B-factor  
column, so a saved project file will retain these calculated values,  
which will be used by other programs when coloring by B-factor or  
temperature (RasMol).

To my knowledge, there is still no single program that contains as  
many features for model validation as does DeepView.

Cheers!