Re: [Jmol-users] Cartoon loop transparency

[Robert H. <ha...@st...>]

They are translucent, but the way they are produced is by a series of
balls, and that is so much duplication of surfaces that they add up to
nearly opaque.

You  can try:

set translucent false

This is a PyMOL-like mode that doesn't allow transparent surfaces to show
through each other. It may work for you. Or you could use

set cartoonsFancy
color cartoons translucent

Bob




On Tue, Nov 5, 2013 at 7:57 AM, Glen van Ginkel <gl...@eb...> wrote:

>  Hi All,
>
> I'm finding that setting cartoon loop transparency works for sheets and
> strands but not for loops.
>
> Is this happening for anyone else.
>
> I'm using the HTML5 viewing option and mostly viewing on chrome on Linux
>
> Kind regards,
>
> Glen
>
>
>
>
> Here is a dump of the console in case it is of use:
>
>
> Jmol._Canvas2D (JSmol) "view_div_2gvz_3"[x]
> call loadScript \atlas\js\libs\jsmol\core\package.js
> call loadScript \atlas\js\libs\jsmol\core\core.z.js -- required by
> ClazzNode
> call loadScript \atlas\js\libs\jsmol\J\awtjs2d\WebOutputChannel.js
> JmolCore.js: synchronous binary file transfer is not available
> Jmol JavaScript applet view_div_2gvz_3_object__862444059923291__
> initializing
> getValue debug = null
> getValue logLevel = null
> getValue allowjavascript = null
> AppletRegistry.checkIn(view_div_2gvz_3_object__862444059923291__)
> call loadScript \atlas\js\libs\jsmol\core\corestate.z.js
> viewerOptions:
> { "name":"view_div_2gvz_3_object","applet":true,"documentBase":
> "http://localhost" <http://localhost>,"platform":"J.awtjs2d.Platform","fullName":"view_div_2gvz_3_object__862444059923291__","progressbar":true,"display":"view_div_2gvz_3_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol.MyStatusListener
> object]","codeBase":"/js/libs/jsmol/j2s/","syncId":"862444059923291","progresscolor":"#66666","bgcolor":"#ffffff"
> }
> (C) 2012 Jmol Development
> Jmol Version: 13.2.7 $Date: 2013-10-01 11:35:15 -0500 (Tue, 01 Oct 2013) $
> java.vendor: j2s
> java.version: 0.0
> os.name: j2s
> Access: ALL
> memory: 0.0/0.0
> processors available: 1
> useCommandThread: false
> appletId:view_div_2gvz_3_object (signed)
> starting HoverWatcher_1
> getValue emulate = null
> defaults = "Jmol"
> getValue boxbgcolor = null
> getValue bgcolor = #ffffff
> backgroundColor = "#ffffff"
> getValue ANIMFRAMECallback = null
> getValue APPLETREADYCallback = Jmol._readyCallback
> APPLETREADYCallback = "Jmol._readyCallback"
> getValue ATOMMOVEDCallback = null
> getValue CLICKCallback = null
> getValue ECHOCallback = null
> getValue ERRORCallback = null
> getValue EVALCallback = null
> getValue HOVERCallback = null
> getValue LOADSTRUCTCallback = null
> getValue MEASURECallback = null
> getValue MESSAGECallback = null
> getValue MINIMIZATIONCallback = null
> getValue PICKCallback = null
> getValue RESIZECallback = null
> getValue SCRIPTCallback = null
> getValue SYNCCallback = null
> getValue STRUCTUREMODIFIEDCallback = null
> getValue doTranslate = null
> language=en_GB
> getValue popupMenu = null
> getValue script = null
> Jmol applet view_div_2gvz_3_object__862444059923291__ ready
> call loadScript \atlas\js\libs\jsmol\core\corescript.z.js
> call loadScript \atlas\js\libs\jsmol\J\script\FileLoadThread.js
> starting QueueThread0_2
> script 1 started
> antialiasDisplay = true
> antialiasTranslucent = true
> debugScript = false
> showScript = 0
> chainCaseSensitive = true
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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