exporting a mineral structure as VRML
Hello, 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? thanks! Janet Iwasa
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
Hi Janet, Those purple dotted lines indicate metal coordination and are not covalent bonds. Apparently the dotted lines don't go into the VRML. You can change them to cylinders by selecting them and using the selection inspector. First ctrl-click on one dotted line. Then press the up-arrow key a few times to select all dotted lines. Then press the selection inspector button in the bottom right corner of the window that says "256 pbonds" (means pseudo-bonds). In the dialog that appears change "bond style" to "stick" and you might also change the radius (maybe from 0.2 to 0.05) so the look different then the real covalent bonds. The stick display of the pseudo-bonds does appear in the VRML. Tom
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
participants (4)
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Eric Pettersen -
Greg Couch -
Janet Iwasa -
Tom Goddard