pymol-users-ad...@lists.sourceforge.net wrote on 02/15/2006 05:36:51 PM: > Hi all, > > There is a beautiful ball-and-stick image on pymol-wiki that I am > trying to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick). > > The wiki image has grey bonds and light blue balls for carbon, dark > blue for nitrogen, and red balls for oxygen. My problem is that all > my bonds and balls are the same color, and I can't figure out how to > make the bonds a grey color, distinct from the atom ball colors. > And I'm trying to script this. >
Hi Marilyn - You probably can't do it all with one object. Create another object which is a duplicate of the one you're working with, then show spheres on object #1 and sticks on object #2. You can then color the balls and the sticks separately, since each object gets its own set of colors. For example: PyMOL>create obj1, 1FLT and chain w Selector: found 797 atoms. Executive: object "obj1" created. PyMOL>create obj2, 1FLT and chain w Selector: found 797 atoms. Executive: object "obj2" created. PyMOL>color gray, obj2 Executive: Colored 797 atoms and 1 object. PyMOL>color green, obj1 Executive: Colored 797 atoms and 1 object. PyMOL>show spheres, obj1 PyMOL>show sticks, obj2 PyMOL>set stick_radius, 0.1 Setting: stick_radius set to 0.10000. PyMOL>set sphere_scale, 0.25 Setting: sphere_scale set to 0.25000. This gives a ball-and-stick of one chain where the balls are all green and the sticks are all gray. Modify as needed.... - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
