By default, PyMOL creates single bonds when joining fragments. To change a bond valence, CTRL-right click on the bond to select it. You should see a "ring" about the bond. Then press CTRL-W to cycle through the possible bond valences: single, double, triple.
Note that it is essentially impossible right now to build complex molecules in PyMOL without using some external molecular minimization and mechanics program, since the "molecular sculpting" feature can only maintain pre-existing atomic geometries. For coarse modeling of protein-ligand interactions, I tend to use PyMOL to draw the initial covalent structures, use MacroModel to perform energy minimization, and then return the structure to PyMOL for purposes modeling the complex. - Warren -- mailto:[email protected] Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -----Original Message----- > From: Guillaume Michaud [mailto:[email protected]] > Sent: Monday, March 11, 2002 12:43 PM > To: [email protected] > Subject: [PyMOL] Create a double bond > > > PLEASE WRITE BACK TO > [email protected] > > Hi, > > I was just wondering how to create a > double bond between two atoms (for > example between a carbon and an oxygen > or C=C). > > Thankx > r1ck5p > -- > > _______________________________________________ > Sign-up for your own FREE Personalized E-mail at Email.com > http://www.email.com/?sr=signup > > Travelocity.com is giving away two million travel miles. > http://ad.doubleclick.net/clk;3969773;6991039;g?http://svc.tra velocity.com/promos/millionmiles_main/0,,TRAVELOCITY,00.html _______________________________________________ PyMOL-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/pymol-users
