[Molvis-list] Errors in Chem Viz

Eric Martz emartz at microbio.umass.edu
Sun Sep 17 17:30:15 EDT 2006

Dear Mario,

I think documenting errors in molecular visualization tools is very 
worthwhile! In FirstGlance in Jmol (http://firstglance.jmol.org) I have 
documented the errors or misinterpretations of chemical structures by the 
Jmol applet (click on All About ... at the main page for a list of 
documentation). Recently, I realized Jmol's "rockets" rendering of beta 
strands is too unrealistic to use (because they are straight, while real 
beta strands are curved). In the next release, this will be dealt with.

Regarding your "errors":

It would help if you number the rows in the table so we could refer to them 
by number.

The "five bonded carbon" is not an error. The dotted "bond" means a 
resonant or partial covalent bond shared with another atom. The carboxyl 
carbon shares a double bond between two oxygens. So it has 1.5 bonds to 
each oxygen. This is elementary chemistry so I would not fault the program 
for not documenting this.

The same happens in the peptide bonds you show in the 2nd item for Arguslab 
vs. Molekel. Neither rendering is ideal. The ideal would be 1.5 bonds to 
both the oxygen and nitrogen. Molekel is ignoring the resonance here (quite 

3POR: I'm not sure what you think is the error here. Also my chemistry may 
not be good enough for this case.

1CRN: I would not fault Chimera for the differences in the end positions. 
These are smoothed traces, so they don't necessarily follow atomic 
positions exactly. They may simply use different anchor points or smoothing 
algorithms. Not really an "error" in my opinion.

Metal bonds: few visualization programs (if any) handle these correctly. I 
agree there are likely errors here, but again, my chemistry is not good enough.

7GPB: the bent TRP is certainly bizzare. I'm not sure if this is an error 
or can be explained by its contacts. By the way, its full name is 
tryptophan not trypsine.

1EW1: both this and the previous and following examples appear to be errors 
in the published PDB files, not errors in the visualization programs. Such 
errors in PDB files are quite common. After all, they are made by people! 
It might be useful to separate the two categories of errors.

One of my favorite errors in a PDB file (because it can be used to test 
people on DNA structure, and to emphasize that not all published data are 
correct) is that one of the base pairs in the DNA in 1D66 is in an 
incorrect (highly unlikely and non-Watson-Crick) conformation. The first 
author confirmed that this is an error they overlooked when publishing it.

Your links to the Practical Model Validation course are broken -- can you 
fix them, please?

I hope you will include Jmol (free, open source, available both as an 
application and as a browser applet) in your tests. There has been 
considerable input from chemists into its development.


At 9/15/06, you wrote:
>I just started a page on "errors in chemistry visualization tools and 
>chemistry data".
>It is available on: <http://www.cscs.ch/~mvalle/ChemViz/errors/index.html>
>The visualization part started as a by-product of testing of existing 
>visualization tools
>to provide guidance to my chemistry users. The Data part collects examples 
>for a course on
>scientific data management that I teach.
>If you have other examples I'm very happy to add them to the page. Also 
>corrections and
>clarifications are welcome (I'm not a chemist...).
>                 mario
>Ing. Mario Valle
>Visualization Group                              | http://www.cscs.ch/~mvalle
>Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
>v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82
>Molvis-list mailing list
>Molvis-list at bioinformatics.org

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