Re: [Jmol-users] JSmol bug?

2013-05-17 Thread Bob Hanson 
Test2.htm doesn't use controls. See testcb.htm in most recent version. 
JSmolControls.js

Sent from my stupid iPhone 

On May 17, 2013, at 8:44 AM, "Spinney, Richard" 
 wrote:

> I have been trying to get JSmol to work and have had a couple of problems. I 
> have a page (build off of the test2.htm demo) that uses the Java applet 
> (https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info.php) , while 
> this displays the PDB and JVXL files correctly, the controls do not appear. I 
> get an error message of “error Jmol.controls undefined” and links to 
> JSmolApi.js. These lead to lines in the code of: “return 
> Jmol.controls._getMenu(….)”; and “return Jmol.control._getCheckbox(…)”.
>  
> I copied this page 
> (https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info-b.php) and 
> changed it to use HTML5 (JSmol.min.js). Again the PDB files are read ok but 
> now the JVXL files don’t work while the controls (menu and checkboxs) do 
> work. The error message on this is “g._applet is null” and points to the 
> JSmol.min.js file.
>  
> I am at a loss on what is wrong here; the calls to the controls are identical 
> between the two pages, as are the load JVXL calls. It does use the serverURL 
> to call jsmol.php and it is version 13.1.16_dev_2013.5.15. Any help would be 
> appreciated.
>  
> Thanks, Rick
> --
> Dr. Richard Spinney
> Department of Chemistry and Biochemistry
> The Ohio State University
> 120A Celeste Laboratory
> 120 West 18th Ave
> Columbus, Ohio 43210
>  
> email: rspin...@chemistry.ohio-state.edu
>  
> Phone:   (614) 247 - 6847
> Fax:   (614) 292 - 1685
>  
> --
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> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
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[Jmol-users] JSmol bug?

2013-05-17 Thread Spinney, Richard 
I have been trying to get JSmol to work and have had a couple of problems. I 
have a page (build off of the test2.htm demo) that uses the Java applet 
(https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info.php) , while this 
displays the PDB and JVXL files correctly, the controls do not appear. I get an 
error message of "error Jmol.controls undefined" and links to JSmolApi.js. 
These lead to lines in the code of: "return Jmol.controls._getMenu()"; and 
"return Jmol.control._getCheckbox(...)".

I copied this page 
(https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info-b.php) and 
changed it to use HTML5 (JSmol.min.js). Again the PDB files are read ok but now 
the JVXL files don't work while the controls (menu and checkboxs) do work. The 
error message on this is "g._applet is null" and points to the JSmol.min.js 
file.

I am at a loss on what is wrong here; the calls to the controls are identical 
between the two pages, as are the load JVXL calls. It does use the serverURL to 
call jsmol.php and it is version 13.1.16_dev_2013.5.15. Any help would be 
appreciated.

Thanks, Rick
--
Dr. Richard Spinney
Department of Chemistry and Biochemistry
The Ohio State University
120A Celeste Laboratory
120 West 18th Ave
Columbus, Ohio 43210

email: 
rspin...@chemistry.ohio-state.edu

Phone:   (614) 247 - 6847
Fax:   (614) 292 - 1685

--
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security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
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Re: [Jmol-users] unable to display rockets visualization on certain PDBs

2013-05-17 Thread Angel Herráez 
Hello Chendra, and welcome to Jmol

All your examples are models taht only have alpha carbons for the 
protein.
On such models, rendering is limited by the lack of other atoms 
(needed for determining orientation of some of the drawing elements).
I am not 100% sure, but I think that for some technical reason 
rockets cannot be calculated or displayed in these circumstances.

If you load full-atom proteins you will have no problem




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[Jmol-users] unable to display rockets visualization on certain PDBs

2013-05-17 Thread Chendra Hadi Suryanto 
Dear all,

I am a new comer in the protein analysis and Jmol.
Currently, I am trying to analyze protein structure through the visualizations 
images using Jmol. In my understanding, rockets visualization in Jmol show the 
secondary structure of alpha helices and beta strands in the shape of directed 
cylinder and arrow. Is it correct? However, occasionally Jmol is unable to 
display rockets visualization on particular protein structures. For example, 
Jmol output blank when I tried to display the rockets visualization of the 
following PDB code: 1EFG, 1NRC, 1DPI, etc.. (many others). 
I would appreciate any comments or suggestions. I am using desktop application 
of Jmol Version 13.0.12.

Thank you,

Best regards,
Chendra--
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Re: [Jmol-users] jmolSetCheckboxGroup problem

2013-05-17 Thread Angel Herráez 

> "HTML5 defines the indeterminate boolean property."
> Apparently works on IE down to v7! (at least, IE7 and IE8 mode in my IE9) -- 
> I'm surprised and reluctant to believe it. But IE9 should be OK

Confirmation: real IE8 also works for this, both in a page with HTML4 
or  HTML5 doctype. 




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