[Jmol-users] RES: Jmol.js checkbox, this.name

[Herráez Sánchez Angel]

Hi Frieda
 
If you cannot solve it like that, why don-t you use getElementById? Since you 
are assigning an id explicitly while calling jmolCheckbox, you could put the 
same id if the javascript call
 
Say
 
jmolCheckbox("javascript myFunction(document.getElementById('myCheckbox'"), 
"javascript myFunction(document.getElementById('myCheckbox')", "myLabel", 
false, "myCheckbox")
 
Then within myFunction() you can extract the name if needed

HTH
 
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Re: [Jmol-users] Continuous Symmetry Measures - A new website

[Herráez Sánchez Angel]

Inbal, I suggest that you add your site to the list existing at Jmol Wiki

http://wiki.jmol.org:81/index.php/Websites_Using_Jmol 

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Re: [Jmol-users] applet size and set pickCallback

[Herráez Sánchez Angel]

Steve, percent-sized div should work, even in Ohio, but there may be browser 
issues limitng it, if I remember correctly. Check out the code of my templates
http://biomodel.uah.es/Jmol/resizable/
I had to set html {height:100%} and body {height:100%} for this to work 
properly in all browsers; maybe that helps you.

~~~
Steven R. Spilatro  wrote:

As you suggested, when sizing the applet in Firefox by percent or 
fractions, the applet must be within a fully qualified div; however, 
the div height must be set to a px value; setting height to a percent 
value does not work -- at least in Ohio.
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Re: [Jmol-users] (no subject)

[Herráez Sánchez Angel]

Eran wrote:
> I'd like to save a state as a script in such a way that when that  
> state-script is recalled on a Jmol applet already displaying  
> something, that state-script will load without affecting the spin- 
> state of the applet 

Hello

Easiest way: if the script is saved to a file, edit it and remove the spin 
command from the state-script.

Otherwise, I think you can use "show spin" to read the spin state before 
calling the state, then issue it after the script.
I did something similar for a "Foolproof spin toggle" you can see at
http://wiki.jmol.org:81/index.php/Recycling_Corner#.22Foolproof.22_spin_toggle
That may give you an idea.

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Re: [Jmol-users] Display 2 or more structures in JMOL

[Herráez Sánchez Angel]

Hi Ravi
 
Yes. there is a command to fix a certain frame/model so that you can see it 
overlayed with any other you choose:
 
 set backgroundModel (integer >= 1) 

Sets a particular model or animation frame to be fixed in place during 
an animation 
  or 
when displaying models loaded 
  from a 
multi-model file. set backgroundModel 0 turns this feature off. Certain 
restrictions apply to scripts when a background model is displayed; in that 
case it may be important to turn the model off and then back on during selected 
scripting. 

 
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[Jmol-users] rockets fails to separate helices

[Herráez Sánchez Angel]

I found a funny behaviour of "rockets" on 2hhd.pdb, chain C

Try this: 

load 2hhd.pdb;

restrict *:C;

select all; spacefill off;

select hetero and not solvent; spacefill on;

select protein; cartoons on; rockets on;

 

There are two stretches of alpha helix separated by a turn around residue nr. 
74. Jmol (both 10.2 and 10.9.87) is assigning an alpha secondary structure to 
the turn. As a consequence, instead of two rockets one gets only one, avoiding 
the full path of the two helices and crossing right through the heme group. 

I know rockets are not meant to be too faithful to structure, but this is 
extreme. Very unpedagogical!

 


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RE: [Jmol-users] Problem loading a pdb file

[Herráez Sánchez Angel]

Hi, Eva
Welcome to Jmol world

Bob's answer is the key; you can read it more detailed in 
http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local


<>

RE: [Jmol-users] CML visualization in Jmol

[Herráez Sánchez Angel]

Hi Francois

What you need is to deactivate autobonding.

On a previos post
http://sourceforge.net/mailarchive/message.php?msg_id=12416924
Miguel sayed:
 Jmol prerelease 10.00.21 is now available 
 It includes support for:
 2.  "set autobond off" can be used before loading any file type to prevent
 auto-bonding. Explicit bonds with the file are retained

This should fix your problem (I have not tested it)
Good luck

<>