Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
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 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 -- 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
[PyMOL] setting the cutoff radius that determines when atoms are bonded
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
Re: [PyMOL] Possible (minor) bug
Hi Joel, thanks for the report. This will be fixed in the next PyMOL release. Cheers, Thomas Joel Tyndall wrote, On 12/03/12 02:53: > Hi Jason/all, > > Possible bug. When measuring distances around coordinated metals, I then > wanted to change the colour of the resulting dashed line. The colour > change would only appear when you turn the object off (or another). > Happens with RNA and protein. > > Cheers > J > > _ > > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > Skype: jtyndall > > Ph: +64 3 479 7293 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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
