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

Eric Martz emartz at microbio.umass.edu
Fri Feb 17 14:00:22 EST 2006

>On Feb 13, 2006, at 1:53 PM, Eric Martz wrote:
>>A new version of FirstGlance in Jmol (http://firstglance.jmol.org)
>>has been released.

At 2/14/06, Gale Rhodes wrote:

>Great job, Eric!
>A couple of things about Jmol itself:
>1) Is it just me, or are Jmol's new (v. 10.00.46) stereographic
>options backward?

You are correct. Stereo is backwards. I noticed this myself about a week 
ago and reported it to jmol-users, so it will be fixed.

>2) One can always think of something to add to these wonderful tools.
>It occurred to me, as I was preparing a talk on judging model
>quality, that Jmol has no built-in options for helping model users to
>validate models.
>         a) Color by B-factor should be a simple addition, and B-factors can
>alert you to certain kinds of model problems.

Good idea. I'll add it.

>  With the same command,
>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.)

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?

>         b) A more useful tool in model validation is a Ramachandran 
> diagram,
>which can expose even some rather subtle model errors, and can be
>useful in sorting out alternative templates for homology modeling.
>Modelers avoid templates that have a lot of Ramachandran outliers.
>The resulting model will have the same outliers.
>         c) Other useful tools would be "Select:Clashing Residues" and
>"Select:Residues with unsatisfied H-bonds." The latter finds buried
>polar side chains that are probably in the wrong place.
>Such errors are present in many PDB files, and occur commonly in
>routine modeling from sequence data using PDB models as templates.
>Viewers that do not have model validation options make all models
>look good, and that's not the truth.

I agree these are very important, but I'm not convinced they should be 
built into Jmol. Rather, I'll add a link (under "More Views..") to the 
Richardson's outstanding MolProbity 
(http://kinemage.biochem.duke.edu/molprobity/index-king.html), which nicely 
handles all of these issues in a java-based viewer (KiNG).

>3) Finally, thanks to Jmol developers for giving what looks like a
>solid foundation for many powerful tools for molecular viewing and

Hear hear!

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