Hi Tobias - It seems to me that you may not have hidden the lines/sticks from the object where you’ve shown the surface. For overlapping objects, the normal non-ray-traced view appears to give precedence to the object that was present in the viewer first. Try disabling and re-enabling your two objects in different orders to see what I mean. Ray, on the other hand, tries to show both at the same time.
There is actually another way to accomplish what you describe in (b). First, you can use the `surface_mode` setting (http://pymolwiki.org/index.php/Surface_mode) to avoid having to modify the flags. Also, instead of creating two objects, the easiest way to have different colors for the surface and the sticks is to use the `surface_color` setting (http://pymolwiki.org/index.php/Surface_color) for your ligand object. set surface_mode, 1 set transparency, 0.5 as sticks, ligand show surface, ligand set surface_color, black, ligand Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 31, 2014, at 8:42 AM, Tobias Beck <tobiasb...@gmail.com<mailto:tobiasb...@gmail.com>> wrote: 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 _______________________________________ ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================
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