I think you have the syntax right. Looks right to me, anyway. I don't know
that you need Jmol.loadFile(). Just create the script:
Jmol.script(jmolApplet0,'load =1blu;display not water;select protein or
nucleic;cartoons only;color structure;select *')
On Sun, Sep 8, 2013 at 8:44 PM, Amjad Farooq <am...@farooqlab.net> wrote:
> Hi Bob,
>
> What is the syntax for placing JSmol commands such as:
>
> Jmol.script(jmolApplet0,'select *;cartoons off;wireframe -0.1')
> and
> Jmol.loadFile(jmolApplet0,'=1blu',';display not water;select protein or
> nucleic;cartoons only;color structure;select *')">
>
> inside a regular javascript. For example:
>
> <script type="text/javascript">
> function pdb {
> // invoke Jmol command
> }
> </script>
>
> <button onClick="pdb();">Click Here</button>
>
>
> Thanks!
> Amjad
>
>
>
>
>
>
>
>
> On Sun, Sep 8, 2013 at 5:36 PM, Amjad Farooq <am...@farooqlab.net> wrote:
>
>> Bob,
>>
>> As you advised, I added the "set the platformSpeed 1" line to the applet
>> when loading PDB file. It improved the speed considerably to a level that I
>> am very happy with. But, I still believe, JSmol somewhat suffers from the
>> speed issue and Jmol is noticeably much more smoother when moving
>> structures around with your mouse.
>>
>> What is the long-term goal? Is JSmol eventually going to replace Jmol? Is
>> the future about having an app that does not rely on an external Java
>> plugin?
>>
>> Just some thoughts.
>>
>> Thank you!
>> Amjad
>>
>>
>>
>>
>> On Sun, Sep 8, 2013 at 4:46 PM, Amjad Farooq <am...@farooqlab.net> wrote:
>>
>>> Bob,
>>>
>>> I tried JSmol on both firefox 23 and chrome under both Fedora 15 and
>>> Windows 7. In all cases, JSmol appeared to be much much slower than Jmol.
>>>
>>> How and where do I set the platform speed? Please advise accordingly.
>>>
>>> Thank you,
>>> Amjad
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Sun, Sep 8, 2013 at 4:02 PM, Robert Hanson <hans...@stolaf.edu>wrote:
>>>
>>>> This is on what platform?
>>>> Did you use
>>>>
>>>> set platformSpeed 1?
>>>>
>>>> Bob
>>>>
>>>>
>>>> On Sun, Sep 8, 2013 at 1:51 PM, Amjad Farooq <amja...@gmail.com> wrote:
>>>>
>>>>> Hi Bob,
>>>>>
>>>>> Just to let you know that I tried the new version of JSmol.
>>>>>
>>>>> JSmol runs very slow when viewing proteins compared to Jmol. So, in
>>>>> short, JSmol is cool if one can do all this without the need for an
>>>>> external Java but the slow speed of JSmol is a big deterrent to using it
>>>>> in
>>>>> everyday work and embedding it in an online web interface to showcase your
>>>>> work.
>>>>>
>>>>> Just some feedback so that it can help you fine tune it further.
>>>>>
>>>>> Thank you for all your time and effort. We appreciate that very much.
>>>>>
>>>>> Regards,
>>>>> Amjad
>>>>>
>>>>>
>>>>> ***************************************************************************************************************************************************
>>>>> *AMJAD FAROOQ PhD DIC | Associate Professor*
>>>>> Dept of Biochemistry & Molecular Biology | Miller School of Medicine |
>>>>> University of Miami | Miami | FL 33136
>>>>> Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217,
>>>>> Miami , FL 33136
>>>>> am...@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax
>>>>> 305-243-3955 | www.farooqlab.net
>>>>>
>>>>> ***************************************************************************************************************************************************
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
>>>>> Discover the easy way to master current and previous Microsoft
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>>>>> _______________________________________________
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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
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
>>>> Discover the easy way to master current and previous Microsoft
>>>> technologies
>>>> and advance your career. Get an incredible 1,500+ hours of step-by-step
>>>> tutorial videos with LearnDevNow. Subscribe today and save!
>>>>
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=58041391&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Jmol-users mailing list
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>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>
>
>
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
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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
------------------------------------------------------------------------------
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Discover the easy way to master current and previous Microsoft technologies
and advance your career. Get an incredible 1,500+ hours of step-by-step
tutorial videos with LearnDevNow. Subscribe today and save!
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