Hi Jared, Thanks a lot for your help and fast response!
Next time I will try to do it as you described, without creating a new object, but for now hiding the sticks for the surface object did the job! Thanks again! Best wishes, Tobias. On Mon, Mar 31, 2014 at 9:33 PM, Sampson, Jared <jared.samp...@nyumc.org>wrote: > 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> 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) > 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. > ================================= > -- _______________________________________ 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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