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
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Verizon Developer Community
>> Take advantage of Verizon's best-in-class app development support
>> A streamlined, 14 day to market process makes app distribution fast and
>> easy
>> Join now and get one step closer to millions of Verizon customers
>> http://p.sf.net/sfu/verizon-dev2dev
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Andy Lu
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and
> easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> 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
------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
