Wow that is really useful!
I run into another problem.
viewer.evalString ("set debugScript;");
viewer.evalString ("set ScriptCallback spacefill ;");
viewer.evalString ("{*}.radius = {*}.temperature.all.mul(0.007);");
So I have put the above code in the paint component, but however I am not
sure of the ScriptCallback "function name" script. Can you help me with it?
Is there like an "if" structure with it? like
if ( viewer.evalString ("set ScriptCallback spacefill ;")) is true
then
viewer.evalString ("{*}.radius = {*}.temperature.all.mul(0.007);");
Thanks once again!
On Fri, Jan 8, 2010 at 3:21 AM, Robert Hanson <[email protected]> wrote:
> If you mean, is there a menu-listener option, the answer is yes. What you
> do is
>
> set debugScript
>
> and then establish a scriptCallback. Usually scripts run from the menu are
> in "quiet" mode, but this debugScript option disables that and reports them
> anyway.
>
> As for setting radius based on BFactors, that is very easy to do. You could
> use
>
> spacefill on
> {*}.radius = {*}.temperature.all
>
> but that will be pretty large. The trick is to use the .mul() function,
> which applies a factor to all of the members of an array individually:
>
> {*}.radius = {*}.temperature.all.mul(0.2)
>
> Another option would be to disable that particular menu item with a custom
> menu so that a user won't think of doing that.
>
> Bob
>
> ps -- note that
>
> {*}.radius = {*}.temperature
>
> by itself first calculates the AVERAGE temperature factor and then applies
> that one number to all the atoms.
>
>
> On Thu, Jan 7, 2010 at 8:25 PM, Andy Lu <[email protected]> wrote:
>
>> Thank you so much for your help.
>> But I have one more question.
>>
>> Is there a way for me to lets say if the user clicks on "ball and stick"
>> viewing format, then I want to change the size of the ball through set
>> percentVdwAtom ()?
>> Because I want to change the size of the ball according to its BFactor and
>> make it so that different ball have different size.
>> I basically need help with the mouse listener function for ball and stick
>> format.
>>
>> Thanks.
>>
>> Or
>>
>> On Thu, Jan 7, 2010 at 4:47 AM, Rolf Huehne <[email protected]>wrote:
>>
>>> On 01/07/2010 04:10 AM, Andy Lu wrote:
>>> > Hi, I am using JMol script within my java application.
>>> >
>>> > I got the select function to work, but how would I go about for invert
>>> > Selection? It's not working for me.
>>> For this purpose you can use the predefined atom set "selected". This
>>> set contains all currently selected atoms. So the command would be:
>>>
>>> select not selected
>>>
>>> Because the "select" command always unselects all atoms that are not
>>> selected by the provided selection expression, the previously selected
>>> atoms are deselected. This way you get the desired inversion.
>>>
>>> Similarly, if you want to add atoms to the current selection, you must
>>> include "selected" in your selection expression, e.g.:
>>>
>>> select selected OR protein
>>>
>>> For details on atom expressions and selections please look at the
>>> interactive scripting documentation:
>>>
>>> http://www.imb-jena.de/ImgLibPDB/Jena3D/doc/jmol_scripting/index.htm#atomexpressions
>>>
>>> http://www.imb-jena.de/ImgLibPDB/Jena3D/doc/jmol_scripting/index.htm#select
>>>
>>> > Also how do I make the selected residues of "Style" -->
>>> "Theme"-->"Trace"
>>> > from the script?
>>> The command is:
>>>
>>> trace on
>>>
>>> See the documentation at
>>>
>>> http://www.imb-jena.de/ImgLibPDB/Jena3D/doc/jmol_scripting/index.htm#trace
>>> for details.
>>>
>>> Regards,
>>> Rolf
>>>
>>>
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>>
>>
>>
>> --
>> Andy Lu
>>
>>
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>>
>
>
> --
> 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
>
>
> ------------------------------------------------------------------------------
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>
>
--
Andy Lu
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