Re: [Jmol-users] Connecting atoms according to the sums of their atom/ionic radii ?

2010-03-04 Thread Alan Hewat
That looks good Bob. I understand that if the atoms are charged according to the CIF file, Jmol will use percentage bounds of the sum of the pairs of ionic radii, either those hard coded into Jmol or those input according to your previous extension. If the atoms are not charged, the bonding radius

Re: [Jmol-users] Connecting atoms according to the sums of their atom/ionic radii ?

2010-03-04 Thread Robert Hanson
Right. If the user has specified {xxx}.ionic = . then those values will be used. On Thu, Mar 4, 2010 at 10:33 AM, Alan Hewat he...@ill.fr wrote: That looks good Bob. I understand that if the atoms are charged according to the CIF file, Jmol will use percentage bounds of the sum of the

[Jmol-users] Mac Question re unbind/bind

2010-03-04 Thread Otis Rothenberger
Hello, I'm using the following start up script to unbind and bind CTRL operations: unbind 'CTRL-LEFT'; bind 'CTRL-LEFT' 'rotateSelected Y _DELTAX;rotateSelected X _DELTAY;';unbind 'CTRL-RIGHT'; bind 'CTRL-RIGHT' 'translateSelected {_DELTAX/100 _DELTAY/-100 0};' Under Windows, the script works

Re: [Jmol-users] MSIE and Jmol bind

2010-03-04 Thread Robert Hanson
where's the page? On Tue, Mar 2, 2010 at 11:50 PM, Otis Rothenberger o...@chemagic.comwrote: Bob, Here is what's not working for me: jmolApplet(450, load /models/alkane!ethane_mm.mol;moveto 0 1 1 1 66;hover off;frank off;set PickCallBack 'processPick';javascript appletLoadedA(), 01)

Re: [Jmol-users] Mac Question re unbind/bind

2010-03-04 Thread Otis Rothenberger
Bob- Very interested! Thanks. How about translate? Otis On Thu, Mar 4, 2010 at 1:53 PM, Robert Hanson hans...@stolaf.edu wrote: Otis, in case you are interested, here is what Jmol does with the standard mouse click motion, in this order though not using exactly this command: rotate X

Re: [Jmol-users] MSIE and Jmol bind

2010-03-04 Thread Otis Rothenberger
Bob, I moved the bind/unbind directly into the Jmol load script. The only thing the javascript function does now is enter some field information after the applet loads, at least that's the intent. Moving the bind/unbind directly into the script solved the bind/unbind problem in MSIE, but MSIE is

Re: [Jmol-users] MSIE and Jmol bind

2010-03-04 Thread Robert Hanson
ignore When I go to your page and execute javascript:alert( appletLoadedA) That reports a function with Firefox but no function with MSIE. Is that what you observe as well? So something in your code is not working. /ignore second part is what I wanted to say. On Thu, Mar 4, 2010 at

[Jmol-users] problem with H-bonds -- a bug?

2010-03-04 Thread Jeff Cohlberg
I am working on a student exercise on lysozyme, file 2LYZ, in which I want the students to see the locations of the helices and sheets in the overall structure.  To get a view of the beta sheet with clearly visibile H-bonds, I type wireframe 100;spacefill off restrict sheet; hbonds

Re: [Jmol-users] Mac Question re unbind/bind

2010-03-04 Thread Jonathan Gutow
Otis, This issue may be that the system binds cntrl-left = right mouse button. This is because until recently most macs came with a one button mouse. I always replaced it with a two-button/scroll-wheel mouse:). But on my mice the cntl-left still brings up the context sensitive