Hi Rye, set connect_cutoff, 0.5
load 1.xyz produces different bonding than if you left the connect_cutoff value to its default, 0.35. Set it to 0.85 and then load the file and you'll see the Unknown atoms in the middle bonded as well. Cheers, -- Jason On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell <ryeterr...@ryeterrell.net> wrote: > > Hi Jason, > > Thanks for the tip. I still couldn't get it to work. I'll google around some > more, but here's the file. Thanks for any help. > > Cheers, > Rye > > > On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees > <jason.vertr...@schrodinger.com> wrote: >> >> Hi Rye, >> >> How about connect_cutoff in Å? There's also connect_mode >> (http://www.pymolwiki.org/index.php/Connect_mode). >> >> If you send me a copy of your file I can look at it. >> >> Cheers, >> >> -- Jason >> >> On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell <ryeterr...@ryeterrell.net> >> wrote: >> > I have a silicon bulk system. Pymol indicates that a handful of the >> > atoms >> > are bonded to each other. Many bonds are not indicated. Is there some >> > value >> > I can adjust that will make pymol indicate that more atoms are bonded? I >> > usually do this by setting some cutoff radius, but googling around has >> > yielded no results. I see that there is a way to bond atom pairs >> > manually, >> > but that would be incredibly tedious given the number of bonds there >> > should >> > be. >> > >> > Thanks for any help! >> > Rye >> > >> > >> > ------------------------------------------------------------------------------ >> > Keep yourself connected to Go Parallel: >> > BUILD Helping you discover the best ways to construct your parallel >> > projects. >> > http://goparallel.sourceforge.net >> > _______________________________________________ >> > 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 >> >> >> >> -- >> Jason Vertrees, PhD >> Director of Core Modeling Product Management >> Schrödinger, Inc. >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 > > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ 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
