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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users