Frank, Yes, PyMOL has molecular editing functions, but it doesn't yet have a clean-up ability.
To rotate bonds, put the mouse into Editing Node and then control-right-click-and-drag on the end of the bond you wish to move. To delete bonds, control right-click and release on the bond, then type Ctrl-D. To add a new bond, ctrl-middle-click on the first atom, ctrl-middle-click on the second, and then type Ctrl-T to add the new bond. If a bond is selected, Ctrl-W will cycle through possible valences. PyMOL does normally connect based on distance if your file does not include connectivity information. If atoms are too close together, then you'll get extra bonds. We don't yet have a pure pattern-based connectivity mode. What kind of files are you finding this problem with most often? Is there an example you can share? Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > S. Frank Yan > Sent: Wednesday, September 22, 2004 10:47 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] modeling in pymol > > Hi, > > I was wondering if PyMOL has some simple modeling > functionalities, such as rotate through a particular bond > (change the dihedral angle), delete/form bonds, superimpose, > etc., via mouse. These functions will be particularly useful > for molecular modeling besides the wonderful graphics. > > Also, when I load certain PDB files, PyMOL automatically > assign many bonds which are not supposed to be there. I > understand it may base on distance rule for assigning > molecular bonds; however, is there any way I can change the > behavior of this? > > Thanks, > Frank > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one > of 170 Project Admins to receive an Apple iPod Mini FREE for > your judgement on who ports your project to Linux PPC the > best. Sponsored by IBM. > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
