Re: [Jmol-users] CML files look flat

[Egon W. <e.w...@sc...>]

Hi Freida,

On Saturday 05 August 2006 20:40, Frieda Reichsman wrote:
> I am starting to learn how to work with CML files. When I opened a
> couple of different cml files in the Jmol application, they displayed
> as completely flat molecules, which clearly they are not. Does this
> indicate a problem with the cml file? Or is there some special way to
> open these files? (I just used the file menu.) I have pasted the
> contents of one file below.

The file you attach indeed only contains 2D coordinates, as indicated by
the x2 and y2 coordinates. The CML attributes for 3D coordinates are x3, y3 
and z3.

Rendering 2D molecules in Jmol is considered bad practice; non-linear 
molecules may indeed look flat. Something obvious to the experienced watcher, 
but confusing at least.

Egon

-- 
e.w...@sc...
Cologne University Bioinformatics Center (CUBIC)
Blog: http://chem-bla-ics.blogspot.com/
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