Hi Marcus et al., You can see which surface model is "first" by looking in the Model Panel. If you want the opposite order than what is listed in the Model Panel, just use the Model Panel to close the one that is listed first. Then when you recreate that surface it will be listed below the other. Example 1d86, with DNA (category main) and netropsin (category ligand). Commands: open 1d86 color yellow main color red ligand set bg_color white surface main surface ligand surftransparency 50 start Model Panel -- the red transparent surface is disappearing behind the yellow transparent surface, and the Model Panel shows the main surface listed above the ligand surface. In the Model Panel, click the line for the main surface on the left and click the "close" button on the right (not the main "Close" button on the bottom!). surface main -- now the main surface is listed lower in the Model Panel and the red ligand surface shows through the yellow main surface I hope this helps, Elaine On Aug 13, 2009, at 6:05 PM, Thomas Goddard wrote:
Hi Marcus,
Unfortunately Chimera does not handle transparency correctly when 2 or more models are transparent. Maybe there is a way to get your two surfaces as pieces of a single surface model which could have there transparency set and would display correctly, but I can't think how. Another trick that would help you is to make the yellow surface have a higher model number so it is drawn after the white surface. With the yellow surface in front that will give more correct appearance as the white transparent surface won't overdraw the yellow one. I guess the surface command is going to produce the same model number as the molecule for both surfaces. Maybe creating the yellow one after the white one will control the drawing order. If that fails you may need to save the 3 residues in a separate PDB and surface it so it can have a distinct model number.
Tom
-------- Original Message -------- Subject: [Chimera-users] displaying two surfaces From: Marcus Carr To: chimera-users@cgl.ucsf.edu Date: 8/13/09 5:50 PM
I am trying to create a figure that encloses three residues in a protein in one surface and the rest of the protein in another. I put the three residues into one group using surfcat and the rest of the protein in another.
When I try adjust the surface transparency, the three-residue surface all but disappears. If I set transparency to 0%, I appears normal. If I increase it even to just 1%, it almost completely disappears. It looks like wherever this three-residue surface is inside the protein surface, it only shows if the transparency of three-residue is set to 0%. All this is with the protein surface set to 50%. I'm not sure whether this list accepts attachments, but I put in screen shots of what it looks like.
marcus
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users