[Chimera-users] exporting a mineral structure as VRML

Greg Couch gregc at cgl.ucsf.edu
Wed Apr 11 11:22:19 PDT 2007

On Wed, 11 Apr 2007, Janet Iwasa wrote:

> I'm trying to use Chimera to export a mineral file (
> http://virtual-museum.soils.wisc.edu/soil_smectite/soil_smectite.pdb) as a
> ball and stick VRML structure, but I'm running into a bit of difficulty
> since some of the bonds don't get made into sticks -- rather, they appear as
> purple dotted lines in the viewer.  Any suggestions on how to get these
> bonds to be made into geometry?

Hi Janet!

There are two ways to convert the dashed lines in the metal coordination 
complexes to sticks:

1) Select one of the lines with the mouse, type the up-arrow key, to 
select all of the similar bonds, then use the selection inspector (button 
at bottom right of main window), to change the bond style to stick.  In 
your example there are three different groups, one each for Al, Fe, and 

2) Use the Tools / General Controls / PseudoBond Panel dialog, select each 
coordination complex in turn and click the attributes... button, then 
click the Component PseudoBond Attributes button to expose the bond style 
option and change the bond style to stick.

Once the dashed lines are converted to sticks, they will export as sticks.

 	- Greg

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