[Chimera-users] exporting a mineral structure as VRML

[Eric Pettersen]

Hi Janet,
	I have also fixed the code to skip forming these metal complexes for  
large inorganic residues.  If you are going to be working with many  
of these files I can send you the fix.

--Eric

On Apr 11, 2007, at 11:22 AM, Greg Couch wrote:

> 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
> Mg.
>
> 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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