Hello: The bond distance is hard coded, as far as I know there is no way to change it without recompiling the program. The "unbond" command works very well though and you can put it into a script when you read in the pdb so that you don't have to redo it every time.
unbond [atom selection 1], [atom selection 2] Cheers, JTM "We can be sure that if a detailed understanding of the molecular basis of chemo-therapeutic activity were to be obtained, the advance of medicine would be greatly accelerated." Linus Pauling, Nobel Laureate 1954 "...everything that living things do can be understood in terms of the jigglings and wigglings of atoms." Richard Feynman, Nobel Laureate 1965 **************************************** Jason Thomas Maynes, MD/PhD Department of Biochemistry and Molecular Biophysics Resident in Anaesthesia and Paediatrics Faculty of Medicine Washington University in St. Louis jmay...@biochem.wustl.edu **************************************** > > Hello, > When I read my .pdb into pymol, for some protein ligands, the program adds > a > bond between two atoms that doesn't exist. I believe that the distances > between these atoms must be under the default cut-off that pymol uses to > define > a bond. Is there a way I can change this defaut number? Is there an easy > way > to get rid of this extra erroneous bond? Any help or suggests would be > greatly > appreciated. > Thanks! > -Brandi > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
