Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
Thanks Thomas. That may or may not have worked, I can't tell. Usually after I load the movie, I can "hide all" followed by "show sticks", and this will show me sticks for all frames of the movie. When I do this now, I get sticks for the first frame, but nothing shows up on later frames. Even if I go to a later frame and type "show sticks", it's all hidden. Of course, if I have to do it for each frame, it's already too much work. Any suggestions for how to accomplish this? Thanks! Rye On Thu, Dec 6, 2012 at 3:02 AM, Thomas Holder wrote: > Hi Rye, > > only "discrete" objects have per state bonding information. Try this: > > load multistate.pdb, discrete=1 > > Hope that helps. > > Cheers, > Thomas > > Rye Terrell wrote, On 12/05/12 18:20: > > I'm loading a movie file now and it appears that the bonds determined in > > the first frame are used throughout the entire movie, even if atoms move > > further apart than the cutoff. Is my perception correct here? If so, can > > I make the bonds be calculated for each frame? > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > > -- > 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 > -- 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
Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
Hi Rye, only "discrete" objects have per state bonding information. Try this: load multistate.pdb, discrete=1 Hope that helps. Cheers, Thomas Rye Terrell wrote, On 12/05/12 18:20: > I'm loading a movie file now and it appears that the bonds determined in > the first frame are used throughout the entire movie, even if atoms move > further apart than the cutoff. Is my perception correct here? If so, can > I make the bonds be calculated for each frame? -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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
Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
I'm loading a movie file now and it appears that the bonds determined in the first frame are used throughout the entire movie, even if atoms move further apart than the cutoff. Is my perception correct here? If so, can I make the bonds be calculated for each frame? On Tue, Dec 4, 2012 at 11:43 AM, Rye Terrell wrote: > Not sure what I was doing wrong before, but that worked like a charm! > Thanks. > > Also, pyMol is really sweet. I've been bugging my group to use it for a > few days now. :D > > Cheers, > Rye > > > On Tue, Dec 4, 2012 at 11:40 AM, Jason Vertrees < > jason.vertr...@schrodinger.com> wrote: > >> 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 >> 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 >> > 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 > > >> >> 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
Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
Not sure what I was doing wrong before, but that worked like a charm! Thanks. Also, pyMol is really sweet. I've been bugging my group to use it for a few days now. :D Cheers, Rye On Tue, Dec 4, 2012 at 11:40 AM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > 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 > 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 > > 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 > >> 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
Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
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 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 > 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 >> 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
Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
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 > 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 > 1.xyz Description: Protein Databank data -- 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
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
