Dear all, I would like to show a transparent surface of a ligand, with the ligand 'inside' as sticks.
I created a new object of the ligand, then tried to show the surface, which fails. With this information here: http://sourceforge.net/p/pymol/mailman/message/27299068/ # do not ignore surfacing of ligands flag ignore, not rep surface # force PyMOL to rebuild the surface rebuild I was then able to show the surface of the ligand. All colors are fine. Transparency is set to 0.5 Now I would like to create an image with ray. However, after ray, there are problems with the color of the ligand sticks inside: a) if the ligand is green and the surface is black, the ligand sticks inside are black as well b) if the surface is black and the ligand carbon atoms are shown in green and other atoms colored by 'color by element', then the non-carbon atoms have their native color with pixels of black (surface color) covering them.... I would like to get b) to work. Any suggestions? Do the commands above (flag ignore) change something for ray? For other surfaces (protein), the above works fine, without any pixels of surface color on the non-carbon atoms. Thank you and best wishes, Tobias. -- _______________________________________ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Vladimir-Prelog-Weg 3, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax: +41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias _______________________________________
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