## jmol-users

 [Jmol-users] Draw polyhedra without central atom From: Nikolay Bogdanov - 2012-09-07 13:16:21 ```I'm trying to make a figure showing the coordination of metal ions in crystal - they form network of tetrahedra. I can do this with bonds, but the figure looks confusing. It would be much more clear with opaque tetrahedrons. As I understand Jmol builds polyhedra around some central atoms, which are missing in my case. So I wonder is there a way to build the polyhedra just from bonds. Thanks, Nikolay ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Angel Herráez - 2012-09-07 16:13:48 Attachments: Message as HTML ```Nikolay, maybe you can add a dummy atom at the center, produce the tetrahedron and then hide the atom. Not very clean, but probably effective I cannot advise however about generating the tetrahedron around the fake atom ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Robert Hanson - 2012-09-07 17:03:25 Attachments: Message as HTML ```The polyhedron needs a central atom. But you can add that yourself. The command appears to be undocumented -- assign {attachmentAtom} "Symbol" {x y z} For example: assign atom {atomno=14} "Cl" {2 3 4} That position {2 3 4} could also be an average position of a number of atoms: assign atom {atomno=14} "Cl" {2 3 4} {atomno=14 or atomno=13 or atomno=12 or atomno=11} then you would also need to do the connections before creating the polyhedra. HOWEVER, with a bit of a tweak of Jmol, I can make this possible without connecting the atoms. You will still need a central atom, though. Let me get back to you on this. Bob On Fri, Sep 7, 2012 at 8:16 AM, Nikolay Bogdanov wrote: > I'm trying to make a figure showing the coordination of metal ions in > crystal - they form network of tetrahedra. I can do this with bonds, but the > figure looks confusing. It would be much more clear with opaque > tetrahedrons. > > As I understand Jmol builds polyhedra around some central atoms, which are > missing in my case. So I wonder is there a way to build the polyhedra just > from bonds. > > Thanks, > Nikolay > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Pshemak Maslak - 2012-09-07 17:24:34 Attachments: Message as HTML ```On 9/7/2012 1:03 PM, Robert Hanson wrote: > The polyhedron needs a central atom. But you can add that yourself. > The command appears to be undocumented -- > > assign {attachmentAtom} "Symbol" {x y z} > > For example: > > assign atom {atomno=14} "Cl" {2 3 4} > > That position {2 3 4} could also be an average position of a number of > atoms: > > assign atom {atomno=14} "Cl" {2 3 4} {atomno=14 or atomno=13 or > atomno=12 or atomno=11} > > then you would also need to do the connections before creating the > polyhedra. > > HOWEVER, with a bit of a tweak of Jmol, I can make this possible > without connecting the atoms. You will still need a central atom, > though. Let me get back to you on this. > > Bob Could the tweak include the option of drawing polyhedra if not all "vertices" are present? Such as a tetrahedron for ammonia or water? Something that would draw a polyhedron when the central atom and a number of vertices is specified with the size equal the specified bond (something like O1 4 O1-H 1 for water).. I know I am asking too much, but if you are tweaking it... Thanks PM > > > On Fri, Sep 7, 2012 at 8:16 AM, Nikolay Bogdanov > > wrote: > > I'm trying to make a figure showing the coordination of metal ions > in crystal - they form network of tetrahedra. I can do this with > bonds, but the > figure looks confusing. It would be much more clear with opaque > tetrahedrons. > > As I understand Jmol builds polyhedra around some central atoms, > which are missing in my case. So I wonder is there a way to build > the polyhedra just > from bonds. > > Thanks, > Nikolay > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest in > malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Robert Hanson - 2012-09-07 18:30:18 Attachments: Message as HTML ```OK, here's how it works. This is probably not documented, but it is the way the state works, so it is fine to use it. All polyhedra need a reference atom, but that atom can be any atom, including one of the face atoms. It doesn't have to be a "central" atom. The key is the (undocumented) TO option: polyhedra ({2}) TO ({2 3 4 5}) The ({...}) notation is an atom "bitset" -- it's a list atom INDEXES (not atom numbers). But realizing now that that's not really necessary, and that maybe this would be useful outside the context of a state, I have this for you: http://chemapps.stolaf.edu/jmol/Jmol-13.zip With this minor revision, now you can use any atom expression: polyhedra {H7} to {H3 or H5 or H6 Or H7} No center here, just faces among the set H3, H5, H6, and H7. The color and display characteristics will depend on H7. Bob On Fri, Sep 7, 2012 at 12:24 PM, Pshemak Maslak wrote: > On 9/7/2012 1:03 PM, Robert Hanson wrote: > > The polyhedron needs a central atom. But you can add that yourself. The > command appears to be undocumented -- > > assign {attachmentAtom} "Symbol" {x y z} > > For example: > > assign atom {atomno=14} "Cl" {2 3 4} > > That position {2 3 4} could also be an average position of a number of > atoms: > > assign atom {atomno=14} "Cl" {2 3 4} {atomno=14 or atomno=13 or atomno=12 > or atomno=11} > > then you would also need to do the connections before creating the > polyhedra. > > HOWEVER, with a bit of a tweak of Jmol, I can make this possible without > connecting the atoms. You will still need a central atom, though. Let me > get back to you on this. > > Bob > > > > Could the tweak include the option of drawing polyhedra if not all > "vertices" are present? Such as a tetrahedron for ammonia or water? > > Something that would draw a polyhedron when the central atom and a number > of vertices is specified with the size equal the specified bond (something > like O1 4 O1-H 1 for water).. > > I know I am asking too much, but if you are tweaking it... > > Thanks > > PM > > > > > > > > > On Fri, Sep 7, 2012 at 8:16 AM, Nikolay Bogdanov > wrote: > >> I'm trying to make a figure showing the coordination of metal ions in >> crystal - they form network of tetrahedra. I can do this with bonds, but the >> figure looks confusing. It would be much more clear with opaque >> tetrahedrons. >> >> As I understand Jmol builds polyhedra around some central atoms, which >> are missing in my case. So I wonder is there a way to build the polyhedra >> just >> from bonds. >> >> Thanks, >> Nikolay >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > > _______________________________________________ > Jmol-users mailing listJmol-users@...nethttps://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Nikolay Bogdanov - 2012-09-11 16:36:34 ```Many thanks ! With the revised version I managed to make the figure. It was a bit laborious because one have to define every tetrahedron (actually a pair is also allowed). One more thing is that atom picking is broken in the modified Jmol version. Though I hope this feature will move to the main branch. The ASSIGN command is also quite useful. Several times I made exactly the same thing, but in much less elegant way. Nikolay On 09/07/12 20:00, Robert Hanson wrote: > OK, here's how it works. This is probably not documented, but it is the > way the state works, so it is fine to use it. > > All polyhedra need a reference atom, but that atom can be any atom, > including one of the face atoms. It doesn't have to be a "central" atom. > The key is the (undocumented) TO option: > > polyhedra ({2}) TO ({2 3 4 5}) > > The ({...}) notation is an atom "bitset" -- it's a list atom INDEXES > (not atom numbers). > > But realizing now that that's not really necessary, and that maybe this > would be useful outside the context of a state, I have this for you: > > http://chemapps.stolaf.edu/jmol/Jmol-13.zip > > With this minor revision, now you can use any atom expression: > > polyhedra {H7} to {H3 or H5 or H6 Or H7} > > No center here, just faces among the set H3, H5, H6, and H7. The color > and display characteristics will depend on H7. > > Bob > > > > On Fri, Sep 7, 2012 at 12:24 PM, Pshemak Maslak > wrote: > > On 9/7/2012 1:03 PM, Robert Hanson wrote: >> The polyhedron needs a central atom. But you can add that >> yourself. The command appears to be undocumented -- >> >> assign {attachmentAtom} "Symbol" {x y z} >> >> For example: >> >> assign atom {atomno=14} "Cl" {2 3 4} >> >> That position {2 3 4} could also be an average position of a >> number of atoms: >> >> assign atom {atomno=14} "Cl" {2 3 4} {atomno=14 or atomno=13 or >> atomno=12 or atomno=11} >> >> then you would also need to do the connections before creating the >> polyhedra. >> >> HOWEVER, with a bit of a tweak of Jmol, I can make this possible >> without connecting the atoms. You will still need a central atom, >> though. Let me get back to you on this. >> >> Bob > > > Could the tweak include the option of drawing polyhedra if not all > "vertices" are present? Such as a tetrahedron for ammonia or water? > > Something that would draw a polyhedron when the central atom and a > number of vertices is specified with the size equal the specified > bond (something like O1 4 O1-H 1 for water).. > > I know I am asking too much, but if you are tweaking it... > > Thanks > > PM > > > > > > >> >> >> On Fri, Sep 7, 2012 at 8:16 AM, Nikolay Bogdanov >> > wrote: >> >> I'm trying to make a figure showing the coordination of metal >> ions in crystal - they form network of tetrahedra. I can do >> this with bonds, but the >> figure looks confusing. It would be much more clear with >> opaque tetrahedrons. >> >> As I understand Jmol builds polyhedra around some central >> atoms, which are missing in my case. So I wonder is there a >> way to build the polyhedra just >> from bonds. >> >> Thanks, >> Nikolay >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. >> Discussions >> will include endpoint security, mobile security and the latest >> in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> -- >> Robert M. Hanson >> Larson-Anderson Professor of Chemistry >> Chair, Chemistry Department >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats.http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> >> >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest in > malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Robert Hanson - 2012-09-11 17:47:35 Attachments: Message as HTML ```details? On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov wrote: > One more thing is that atom picking is broken in the modified Jmol > version. -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Nikolay Bogdanov - 2012-09-11 19:41:47 Attachments: Message as HTML ```It is unable to select atoms using mouse, and there is no hint with atom ID and number when cursor hangs at atom. Rotation with left click, and right click menu work. Same on both mac os and linux. 2012/9/11 Robert Hanson > details? > > > On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov < > nikol.bogdanov@...> wrote: > > >> One more thing is that atom picking is broken in the modified Jmol >> version. > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Robert Hanson - 2012-09-12 00:09:21 Attachments: Message as HTML ```working OK for me. Is this app or applet? What script commands are you giving Jmol to request "select atoms with the mouse"? On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov wrote: > It is unable to select atoms using mouse, and there is no hint with atom > ID and number when cursor hangs at atom. Rotation with left click, and > right click menu work. Same on both mac os and linux. > > 2012/9/11 Robert Hanson > >> details? >> >> >> On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov < >> nikol.bogdanov@...> wrote: >> >> >>> One more thing is that atom picking is broken in the modified Jmol >>> version. >> >> >> >> >> -- >> Robert M. Hanson >> Larson-Anderson Professor of Chemistry >> Chair, Chemistry Department >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Pshemak Maslak - 2012-09-12 00:29:03 Attachments: Message as HTML ``` On 9/11/2012 8:09 PM, Robert Hanson wrote: > working OK for me. Is this app or applet? What script commands are you > giving Jmol to request "select atoms with the mouse"? Tested on the *desktop only* 13.1.4 HOLD (2012-9-8) with .spartan files The atom labels do not show on hover. The files cannot be dragged into Jmol (they do load with script "load"). on XP, files with space in their name cannot be dragged on win 7 PM. > > On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov > > wrote: > > It is unable to select atoms using mouse, and there is no hint > with atom ID and number when cursor hangs at atom. Rotation with > left click, and right click menu work. Same on both mac os and linux. > > 2012/9/11 Robert Hanson > > > details? > > > On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov > > > wrote: > > One more thing is that atom picking is broken in the > modified Jmol version. > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest > in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest in > malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Nikolay Bogdanov - 2012-09-13 13:38:59 ```I use .jar file of Jmol 13.1.4_HOLD (2012-09-08 11:05) with .xyz and .cif files. I tried following commands, as well as selecting from the menu: set picking atom set picking site Distance and angle measurements also not working. NB On 09/12/12 02:09, Robert Hanson wrote: > working OK for me. Is this app or applet? What script commands are you > giving Jmol to request "select atoms with the mouse"? > > On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov > > wrote: > > It is unable to select atoms using mouse, and there is no hint with > atom ID and number when cursor hangs at atom. Rotation with left > click, and right click menu work. Same on both mac os and linux. > > 2012/9/11 Robert Hanson > > > details? > > > On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov > > wrote: > > One more thing is that atom picking is broken in the > modified Jmol version. > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest > in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest in > malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Robert Hanson - 2012-09-13 16:16:16 Attachments: Message as HTML ```Isn't the latest version 13.1.5? On Tue, Sep 11, 2012 at 7:29 PM, Pshemak Maslak wrote: > ** > On 9/11/2012 8:09 PM, Robert Hanson wrote: > > working OK for me. Is this app or applet? What script commands are you > giving Jmol to request "select atoms with the mouse"? > > > Tested on the *desktop only* 13.1.4 HOLD (2012-9-8) with .spartan files > > The atom labels do not show on hover. > Yes, I think I fixed that, though. They are there, but one line too high. > > The files cannot be dragged into Jmol (they do load with script "load"). > on XP, files with space in their name cannot be dragged on win 7 > > Ah. Interesting. > PM. > > > > > > > > > On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov < > nikol.bogdanov@...> wrote: > >> It is unable to select atoms using mouse, and there is no hint with atom >> ID and number when cursor hangs at atom. Rotation with left click, and >> right click menu work. Same on both mac os and linux. >> >> 2012/9/11 Robert Hanson >> >>> details? >>> >>> >>> On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov < >>> nikol.bogdanov@...> wrote: >>> >>> >>>> One more thing is that atom picking is broken in the modified Jmol >>>> version. >>> >>> >>> >>> >>> -- >>> Robert M. Hanson >>> Larson-Anderson Professor of Chemistry >>> Chair, Chemistry Department >>> St. Olaf College >>> Northfield, MN >>> http://www.stolaf.edu/people/hansonr >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmol-users@... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > _______________________________________________ > Jmol-users mailing listJmol-users@...nethttps://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Nikolay Bogdanov - 2012-09-14 14:20:44 ```Everything works fine for me with the latest Jmol 13.1.4 (2012-09-09 00:32). As well as extended polyhedra command. On 09/13/12 18:16, Robert Hanson wrote: > Isn't the latest version 13.1.5? > > On Tue, Sep 11, 2012 at 7:29 PM, Pshemak Maslak > wrote: > > __ > On 9/11/2012 8:09 PM, Robert Hanson wrote: >> working OK for me. Is this app or applet? What script commands are >> you giving Jmol to request "select atoms with the mouse"? > > Tested on the *desktop only* 13.1.4 HOLD (2012-9-8) with .spartan files > > The atom labels do not show on hover. > > > Yes, I think I fixed that, though. They are there, but one line too high. > > > The files cannot be dragged into Jmol (they do load with script > "load"). on XP, files with space in their name cannot be dragged on > win 7 > > Ah. Interesting. > > PM. > > > > > > > >> >> On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov >> > wrote: >> >> It is unable to select atoms using mouse, and there is no hint >> with atom ID and number when cursor hangs at atom. Rotation >> with left click, and right click menu work. Same on both mac >> os and linux. >> >> 2012/9/11 Robert Hanson > > >> >> details? >> >> >> On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov >> > > wrote: >> >> One more thing is that atom picking is broken in the >> modified Jmol version. >> ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Pshemak Maslak - 2012-09-14 17:39:39 Attachments: Message as HTML ```On 9/13/2012 12:16 PM, Robert Hanson wrote: > Isn't the latest version 13.1.5? I am confused. Where can I find 13.1.5? The "bleeding edge" ( http://chemapps.stolaf.edu/jmol/) is 13.1.4 HOLD 2012. PM > > On Tue, Sep 11, 2012 at 7:29 PM, Pshemak Maslak > wrote: > > On 9/11/2012 8:09 PM, Robert Hanson wrote: >> working OK for me. Is this app or applet? What script commands >> are you giving Jmol to request "select atoms with the mouse"? > > Tested on the *desktop only* 13.1.4 HOLD (2012-9-8) with .spartan > files > > The atom labels do not show on hover. > > > Yes, I think I fixed that, though. They are there, but one line too high. > > > The files cannot be dragged into Jmol (they do load with script > "load"). on XP, files with space in their name cannot be dragged > on win 7 > > Ah. Interesting. > > PM. > > > > > > > >> >> On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov >> > wrote: >> >> It is unable to select atoms using mouse, and there is no >> hint with atom ID and number when cursor hangs at atom. >> Rotation with left click, and right click menu work. Same on >> both mac os and linux. >> >> 2012/9/11 Robert Hanson > > >> >> details? >> >> >> On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov >> > > wrote: >> >> One more thing is that atom picking is broken in the >> modified Jmol version. >> >> >> >> >> -- >> Robert M. Hanson >> Larson-Anderson Professor of Chemistry >> Chair, Chemistry Department >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, >> 1900 >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's >> security and >> threat landscape has changed and how IT managers can >> respond. Discussions >> will include endpoint security, mobile security and the >> latest in malware >> threats. >> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. >> Discussions >> will include endpoint security, mobile security and the >> latest in malware >> threats. >> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> -- >> Robert M. Hanson >> Larson-Anderson Professor of Chemistry >> Chair, Chemistry Department >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats.http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> >> >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest in > malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users ```
 Re: [Jmol-users] Draw polyhedra without central atom From: Robert Hanson - 2012-09-14 22:22:27 Attachments: Message as HTML ```Oh, OK. Well, we'll get that fixed..... On Fri, Sep 14, 2012 at 12:39 PM, Pshemak Maslak wrote: > On 9/13/2012 12:16 PM, Robert Hanson wrote: > > Isn't the latest version 13.1.5? > > > I am confused. Where can I find 13.1.5? > > The "bleeding edge" ( http://chemapps.stolaf.edu/jmol/) is 13.1.4 HOLD > 2012. > > PM > > > > > On Tue, Sep 11, 2012 at 7:29 PM, Pshemak Maslak wrote: > >> On 9/11/2012 8:09 PM, Robert Hanson wrote: >> >> working OK for me. Is this app or applet? What script commands are you >> giving Jmol to request "select atoms with the mouse"? >> >> >> Tested on the *desktop only* 13.1.4 HOLD (2012-9-8) with .spartan files >> >> The atom labels do not show on hover. >> > > Yes, I think I fixed that, though. They are there, but one line too high. > > >> >> The files cannot be dragged into Jmol (they do load with script "load"). >> on XP, files with space in their name cannot be dragged on win 7 >> >> Ah. Interesting. > > > >> PM. >> >> >> >> >> >> >> >> >> On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov < >> nikol.bogdanov@...> wrote: >> >>> It is unable to select atoms using mouse, and there is no hint with atom >>> ID and number when cursor hangs at atom. Rotation with left click, and >>> right click menu work. Same on both mac os and linux. >>> >>> 2012/9/11 Robert Hanson >>> >>>> details? >>>> >>>> >>>> On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov < >>>> nikol.bogdanov@...> wrote: >>>> >>>> >>>>> One more thing is that atom picking is broken in the modified Jmol >>>>> version. >>>> >>>> >>>> >>>> >>>> -- >>>> Robert M. Hanson >>>> Larson-Anderson Professor of Chemistry >>>> Chair, Chemistry Department >>>> St. Olaf College >>>> Northfield, MN >>>> http://www.stolaf.edu/people/hansonr >>>> >>>> >>>> If nature does not answer first what we want, >>>> it is better to take what answer we get. >>>> >>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. >>>> Discussions >>>> will include endpoint security, mobile security and the latest in >>>> malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmol-users@... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmol-users@... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> -- >> Robert M. Hanson >> Larson-Anderson Professor of Chemistry >> Chair, Chemistry Department >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> >> >> _______________________________________________ >> Jmol-users mailing listJmol-users@...nethttps://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > > _______________________________________________ > Jmol-users mailing listJmol-users@...nethttps://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ```