[Jmol-users] JSmol2wp 0.94 beta on GitHub

[Jim Hu]

Thanks to feedback from Henry Rzepa, I've made some more changes to the 
JSmol2wp wordpress plugin. A zip of this version is at GitHub 

https://github.com/jimhu-tamu/wordpress/tree/master/plugins

and I've moved the demo to a more stable URL:

http://biochemistry.tamu.edu/jsmol2wp/

Key changes:
- added a parameter to load an isosurface
- I hope it does a better job of guessing the default rendering option from 
what you load. 
- wrote my own function to find the correct attachments - now it should not be 
confused by two items in the media library with the same filename but different 
extensions
- squashed a very odd bug where captions with spaces were not matching in a 
string comparison unless something that I thought was already a string was 
explicitly recast as a string. 

As you can see, the version numbers are asymptotically approaching 1.0, which 
I'm saving for when it's ready to be released on wordpress.org.

Jim
=
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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Re: [Jmol-users] bmv viewer performance

[Rolf Huehne]

Am 23.06.14 20:19, schrieb Ravi Raja Merugu:
>
> Thanks for the suggestions..
>
> On 23 June 2014 20:25, Rolf Huehne  > wrote:
> I also tested it with Safari on MacOS.
> The original URL (http://www.rsquarelabs.com/bmv) didn't work at all
> there. At the end of the URL was appended a slash about ten times
> (waiting 1-2 seconds in between) and then Safari reported that there
> were too many redirections to the same URL. (Only the error message was
> shown, no viewer).
>
>
> Thanks for raising this issue, Could you please check with the url
> http://rsquarelabs.com/bmv.php , and let me know if the same behaviour
> exists
>
This URL is ok in Safari since it is essentially the same URL as the one 
I used for testing in Safari (just lacking the extra options).

Regards,
Rolf

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Re: [Jmol-users] File name and version number

[Bob Hanson]

That is correct. And since most of the daily work is done on 14.3, not 14.2, it 
should not be too often that 14.2 gets updated. 

Bob


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Re: [Jmol-users] bmv viewer performance

[Ravi Raja Merugu]

On 23 June 2014 23:44, Robert Hanson  wrote:

> I think the main problem with this page is the version:
>
> ___JmolDate="$Date: 2014-02-12 19:13:05 -0600 (Wed, 12 Feb 2014) $"
> ___JmolVersion="14.1.8"
>
> That is 10 versions behind. I would not test anything with it.
>

Thanks, I will update it soon.


>
> Bob
>
>
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>



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Re: [Jmol-users] bmv viewer performance

[Ravi Raja Merugu]

Thanks for the suggestions..

On 23 June 2014 20:25, Rolf Huehne  wrote:

> On 06/20/2014 06:14 PM, Ravi Raja Merugu wrote:
> > On 20 June 2014 21:26, Rolf Huehne  wrote:
> >> Is there a way to force Java mode?
> >>
> >
> > try  http://rsquarelabs.com/bmv.php?_USE=JAVA , it should force the
> viewer
> > to use JAVA engine.
> >
> I tried it and it lacked most of the delays of the HTML5 version.
> Loading PDB entry 1DEH took about 3 seconds instead of 30.
>

as i said. JAVA works much faster


>
> In contrast to the HTML5 version the popup menu was available. so you
> didn't deactivate it on the HTML5 version on purpose and it is a bug
> that it doesn't work there?
>

I didnt deactivate anything, I think JAVA version of the viewer has a java
based dialog box, which we see from Jmol.  But , HTML5 version of the
viewer uses HTML and JS as the dialog box, which I think might go through
further developments in future versions.


>
> Selected atoms were indicated by a yellow halo with Java but not with
> HTML5. But I couldn't find any way to deactivate the selection halos.
> This makes working with the viewer very difficult if all atoms are
> selected and you can see almost only halos and no details of the
> rendered structure.
>

I will add an option for enable/disable the halos..


>
> I also tested it with Safari on MacOS.
> The original URL (http://www.rsquarelabs.com/bmv) didn't work at all
> there. At the end of the URL was appended a slash about ten times
> (waiting 1-2 seconds in between) and then Safari reported that there
> were too many redirections to the same URL. (Only the error message was
> shown, no viewer).
>

Thanks for raising this issue, Could you please check with the url
http://rsquarelabs.com/bmv.php , and let me know if the same behaviour
exists


>
> Since I don't have Java installed yet on my MacBook I replaced 'JAVA' in
> the second URL (http://rsquarelabs.com/bmv.php?_USE=JAVA) by 'HTML5'.
> The interface looked different here (compared to Firefox on Linux).
>

Yes actually its a responsive design, The drop down menus style can be seen
only in Firefox, its is because of some issues with dropbox menus over java
applets in rest of the browsers(other than Firefox). So all the other
browsers load with the different layout(unlike Firefox layout) as u
mentioned


> There was no dropdown menu at the top but an accordeon menu at the left
> side. I actually liked this better than the pulldown menu because the
> subselections in a single menu line made much more sense here. This way
> they will presumably not be very confusing. But what I didn't liked was
> that only one part of the menu can be open at a time. This will be very
> annoying because it will presumably happen quite often that a user will
> need functions from different parts quite frequently. I would recommend
> to let the user decide which menu parts should be open/closed.
>

I will consider this and will work on making menus more user-friendly
pretty soon.


>
> The delays were similar to those with Firefox on Linux.
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
>
> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
>
> Phone:   +49 3641 65 6205
> Fax: +49 3641 65 6210
> E-Mail:  rhue...@fli-leibniz.de
> Website: http://www.fli-leibniz.de
>
>Scientific Director: Prof. Dr. K. Lenhard Rudolph
> Head of Administration: Dr. Daniele Barthel
> Chairman of Board of Trustees: Dennys Klein
>
> VAT No: DE 153 925 464
> Register of Associations: No. 230296, Amtsgericht Jena
> Tax Number: 162/141/08228
>
>
>
> --
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
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>



-- 
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Molecular Modeller & Web Developer
http://www.rsquarelabs.com
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Re: [Jmol-users] bmv viewer performance

[Robert Hanson]

I think the main problem with this page is the version:

___JmolDate="$Date: 2014-02-12 19:13:05 -0600 (Wed, 12 Feb 2014) $"
___JmolVersion="14.1.8"

That is 10 versions behind. I would not test anything with it.

Bob

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Re: [Jmol-users] bmv viewer performance

[Rolf Huehne]

On 06/20/2014 06:14 PM, Ravi Raja Merugu wrote:
> On 20 June 2014 21:26, Rolf Huehne  wrote:
>> Is there a way to force Java mode?
>>
>
> try  http://rsquarelabs.com/bmv.php?_USE=JAVA , it should force the viewer
> to use JAVA engine.
>
I tried it and it lacked most of the delays of the HTML5 version. 
Loading PDB entry 1DEH took about 3 seconds instead of 30.

In contrast to the HTML5 version the popup menu was available. so you 
didn't deactivate it on the HTML5 version on purpose and it is a bug 
that it doesn't work there?

Selected atoms were indicated by a yellow halo with Java but not with 
HTML5. But I couldn't find any way to deactivate the selection halos. 
This makes working with the viewer very difficult if all atoms are 
selected and you can see almost only halos and no details of the 
rendered structure.

I also tested it with Safari on MacOS.
The original URL (http://www.rsquarelabs.com/bmv) didn't work at all 
there. At the end of the URL was appended a slash about ten times 
(waiting 1-2 seconds in between) and then Safari reported that there 
were too many redirections to the same URL. (Only the error message was 
shown, no viewer).

Since I don't have Java installed yet on my MacBook I replaced 'JAVA' in 
the second URL (http://rsquarelabs.com/bmv.php?_USE=JAVA) by 'HTML5'.
The interface looked different here (compared to Firefox on Linux).
There was no dropdown menu at the top but an accordeon menu at the left 
side. I actually liked this better than the pulldown menu because the 
subselections in a single menu line made much more sense here. This way 
they will presumably not be very confusing. But what I didn't liked was 
that only one part of the menu can be open at a time. This will be very 
annoying because it will presumably happen quite often that a user will 
need functions from different parts quite frequently. I would recommend 
to let the user decide which menu parts should be open/closed.

The delays were similar to those with Firefox on Linux.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein

VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228


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Re: [Jmol-users] File name and version number

[Peter Brommer]

Hi all,

thanks for clarification. I got confused by the upgrade to 14.2.0 (had 
forgotten that the earlier versions this month had been 14.0.17) and so 
panicked when I found that directory empty of earlier versions. Sorry about 
that.

So just to be sure: Current stable version is 14.2.0_2014.06.13, and that file 
will be around unless something is catastrophically wrong with that file. This 
I could definitely make work.

Peter



On 21 Jun 2014, at 00:24, Robert Hanson  wrote:

> The plan is to leave the daily binaries up on SourceForge UNLESS there is a 
> critical error that necesitates removing one from consideration. I hope not 
> to have to do that. Bear with me if I do. I suggest giving 24 to 48 hours 
> buffer between your loading the latest version into the MacPort if possible.
> 
> I will check the ANT task and see if it is adding to or overwriting the 
> directories. Maybe it is deleting older versions. But I don´t think it is, as 
> there are two daily versions in 
> http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.17
> 
> I think it is important to do it this way. It has worked far better for me to 
> have the date stamp in the version. If necessary we can increment the third 
> component every time, but sometimes these are coming so fast, more than one 
> per day, that I hate to do that. 
> 
> I am sensitive to the issue, but it is possible to infer the latest version 
> from the page based on the Looking for the latest version link. 
> 
> Bob
> 
> 
> 
> 
> Bob
> 
> 
> 
> On Fri, Jun 20, 2014 at 7:44 AM, Rolf Huehne  wrote:
> On 06/20/2014 12:49 PM, Angel Herráez wrote:
> > Peter,
> >
> > Daily releases at StOlaf server are certainly not something to point
> > to in an automated way, in my opinion.
> > You should only target releases at SourceForge, which are not so
> > frequent and do no disappear --at least if they are not broken.
> >
> Angel, I don't think Peter is referring to releases at StOlaf.
> Quote:
> "1) Leave all daily binaries up on sourceforge."
> 
> The version numbering scheme was changed, including now a date stamp
> after the three numbers. This is reflected necessarily also at
> sourceforge. Otherwise the file names wouldn't be unique for a specific
> release.
> Example
> (http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.17/):
>Jmol-14.0.17_2014.06.11-full.tar.gz
>Jmol-14.0.17_2014.06.10-full.tar.gz
> 
> Including a date stamp into a version numbering scheme is kind of a
> nightmare for people (like Peter) who have to keep track of new versions
> automatically because new version numbers become unpredictable.
> (I know what I am speaking of because we maintain a number of automatic
> updates from external databases used as data sources for our 3D
> structure database JenaLib. Finding new releases automatically can be
> such a pain!)
> 
> I can see that it might be helpful for a developer to include a date
> stamp because it might make it easier not to mix up different versions.
> Especially if they are emerging very frequently.
> But besides the question if a date stamp should be part of a version
> numbering system, there is also another point:
> Is it really necessary to add a fourth level? Aren't three levels
> already a lot and already sufficient?
> 
> Regards,
> Rolf
> 
> --
> 
> Rolf Huehne
> Postdoc
> 
> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
> 
> Phone:   +49 3641 65 6205
> Fax: +49 3641 65 6210
> E-Mail:  rhue...@fli-leibniz.de
> Website: http://www.fli-leibniz.de
> 
>Scientific Director: Prof. Dr. K. Lenhard Rudolph
> Head of Administration: Dr. Daniele Barthel
> Chairman of Board of Trustees: Dennys Klein
> 
> VAT No: DE 153 925 464
> Register of Associations: No. 230296, Amtsgericht Jena
> Tax Number: 162/141/08228
> 
> 
> --
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
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> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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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