## Re: [Jmol-users] question about draw cylinder function in jmol

 Re: [Jmol-users] question about draw cylinder function in jmol From: I B - 2009-08-31 18:58:04 Attachments: Message as HTML ```Thanks Angel, Circle has limited capabilities, unlike cylinder, for plane presenting, but atomno=X is definetly something to practice with. We have two more questions, we are looking for jmol functions: a) function that gets the effect of: right click on jmol applet -> Style -> Labels -> With Atom Number; b) function that gets the effect of: right click on jmol applet -> Style -> Scheme -> Wireframe Ball and Stick (which is the normal view). are there jmol functions that can do these things? something we can put behind the button/checkbox? Thank you very much for your help, Ira and Yael. 2009/8/30 Angel Herráez > Hello > > > We've been changing the coordinates and it changes the position of the > plane, > > just wondering ifthere is some constancy in it, > > Certainly there is! You will need some math to figure out the axis you > need. > > > Maybe you can do it easier using CIRCLE instead of CYLINDER. > Try the attached model with these commands: > > load ala.mol2 > draw plane1_disk circle width 2.2 {atomno=5} {(atomno=10,atomno=11)} > draw plane2_disk circle width 2.2 {atomno=5} {(atomno=10,atomno=12)} > draw plane3_disk circle width 2.2 {atomno=5} {(atomno=11,atomno=12)} > > or > load ala.mol2 > draw plane1_disk circle width 2.2 {atomno=5} {16.819 -9.437 -0.764} > draw plane2_disk circle width 2.2 {atomno=5} {15.197 -9.615 -0.785} > draw plane3_disk circle width 2.2 {atomno=5} {15.918 -8.579 -1.821} > > > The first coordiante is the center of the circle/disk, the second is a > point giving the > orientation normal to the disk (in the first set, the middle point between > two atoms; in the > second, just a coordinate, either calculated or picked from an atom) > > > > The following section of this message contains a file attachment > prepared for transmission using the Internet MIME message format. > If you are using Pegasus Mail, or any other MIME-compliant system, > you should be able to save it or view it from within your mailer. > If you cannot, please ask your system administrator for assistance. > > ---- File information ----------- > File: ala.mol2 > Date: 19 Jul 2009, 2:48 > Size: 1663 bytes. > Type: Unknown > > ```

 [Jmol-users] question about draw cylinder function in jmol From: I B - 2009-08-16 10:22:43 Attachments: Message as HTML ``` Hi, We're working with this function - draw cylinder in jmol, and we don't know how to use it properly with all it's parameters. Can you please send us the possible parameters of this function? Mostly we're interested in parameters that are related to location of the cylinder, through points or angels. Thanks, Ira and Yael. ```
 Re: [Jmol-users] question about draw cylinder function in jmol From: I B - 2009-08-31 18:58:04 Attachments: Message as HTML ```Thanks Angel, Circle has limited capabilities, unlike cylinder, for plane presenting, but atomno=X is definetly something to practice with. We have two more questions, we are looking for jmol functions: a) function that gets the effect of: right click on jmol applet -> Style -> Labels -> With Atom Number; b) function that gets the effect of: right click on jmol applet -> Style -> Scheme -> Wireframe Ball and Stick (which is the normal view). are there jmol functions that can do these things? something we can put behind the button/checkbox? Thank you very much for your help, Ira and Yael. 2009/8/30 Angel Herráez > Hello > > > We've been changing the coordinates and it changes the position of the > plane, > > just wondering ifthere is some constancy in it, > > Certainly there is! You will need some math to figure out the axis you > need. > > > Maybe you can do it easier using CIRCLE instead of CYLINDER. > Try the attached model with these commands: > > load ala.mol2 > draw plane1_disk circle width 2.2 {atomno=5} {(atomno=10,atomno=11)} > draw plane2_disk circle width 2.2 {atomno=5} {(atomno=10,atomno=12)} > draw plane3_disk circle width 2.2 {atomno=5} {(atomno=11,atomno=12)} > > or > load ala.mol2 > draw plane1_disk circle width 2.2 {atomno=5} {16.819 -9.437 -0.764} > draw plane2_disk circle width 2.2 {atomno=5} {15.197 -9.615 -0.785} > draw plane3_disk circle width 2.2 {atomno=5} {15.918 -8.579 -1.821} > > > The first coordiante is the center of the circle/disk, the second is a > point giving the > orientation normal to the disk (in the first set, the middle point between > two atoms; in the > second, just a coordinate, either calculated or picked from an atom) > > > > The following section of this message contains a file attachment > prepared for transmission using the Internet MIME message format. > If you are using Pegasus Mail, or any other MIME-compliant system, > you should be able to save it or view it from within your mailer. > If you cannot, please ask your system administrator for assistance. > > ---- File information ----------- > File: ala.mol2 > Date: 19 Jul 2009, 2:48 > Size: 1663 bytes. > Type: Unknown > > ```
 Re: [Jmol-users] question about draw cylinder function in jmol From: Robert Hanson - 2009-09-01 12:08:22 Attachments: Message as HTML ```Actually, with Jmol 11.8, draw CIRCLE is much expanded. It now draws circles (and ARC draws rings) in any orientation. I've updated the documentation at http://chemapps.stolaf.edu/jmol/docs/#draw to be clearer about that. Bob ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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] question about draw cylinder function in jmol From: Paul Pillot - 2009-08-31 20:03:53 ```> we are looking for jmol functions: > > a) function that gets the effect of: right click on jmol applet -> > Style -> Labels -> With Atom Number; label %i > b) function that gets the effect of: right click on jmol applet -> > Style -> Scheme -> Wireframe > > Ball and Stick > (which is the normal view). spacefill 20%; wireframe 0.15 Paul ```
 Re: [Jmol-users] question about draw cylinder function in jmol From: I B - 2009-08-31 20:25:23 Attachments: Message as HTML ```Thank you very much!! On Mon, Aug 31, 2009 at 10:48 PM, Paul Pillot < paul.pillot@...> wrote: > > we are looking for jmol functions: > > > > a) function that gets the effect of: right click on jmol applet -> > > Style -> Labels -> With Atom Number; > label %i > > b) function that gets the effect of: right click on jmol applet -> > > Style -> Scheme -> Wireframe > > > > Ball and Stick > > (which is the normal view). > spacefill 20%; wireframe 0.15 > > Paul > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > ```