[Jmol-users] Fwd: Jmol-users Digest, Vol 133, Issue 3

[Craig T Martin]

Henry

   I just checked the most recent Safari Developer Preview (32), running under 
Sierra.
Release 32 (Safari 11.0, WebKit 12604.1.23.0.4)

   Java is supported. I’ve sent you two screenshots showing this.

   I provide this only for clarity. I share your concern that Apple may very 
well ban Java in the near future. And with good reason...

Best regards

Craig

PS - I am very impressed by JSMol on my Mac - I have a very large and complex 
protein and it zips along! So as soon as I catch up on porting things to JSmol, 
I’ll be happy to see Java support go away.

  (sadly, JSmol is not so fast on my iPad Pro…)

> Begin forwarded message:
> 
> From: jmol-users-requ...@lists.sourceforge.net 
> 
> Subject: Jmol-users Digest, Vol 133, Issue 3
> Date: June 8, 2017 at 8:18:53 AM EDT
> To: jmol-users@lists.sourceforge.net 
> Reply-To: jmol-users@lists.sourceforge.net 
> 
> 
> Message: 5
> Date: Thu, 8 Jun 2017 10:29:56 +
> From: "Rzepa, Henry S"  >
> To: " >"
>    >
> Cc: "Rzepa, Henry S" >
> Subject: [Jmol-users] Java will go from Safari as well as already gone
>   from Opera, FF and Chrome
> Message-ID:  >
> Content-Type: text/plain; charset="utf-8"
> 
> I have had a look at Safari preview 32.  In the preferences/security tab, the 
> current production safari has settings for
> 
> 1. Allow WebGL
> 2. Allow Internet Plugins,  and in this latter one can configure to allow  
> Java.
> 
> In Safari 32, both of these are now gone.   With  High Sierra developer 
> preview about to be released into  beta, may bring confirmation that  Safari 
> too has now not merely been deprecated but disallowed. 
> 
> If correct, this means that Jmol.jar can only now run in application mode, 
> and not as a browser plugin. 
> 
> Still,  Apple promise that the new Safari will be  ?faster?, although  I 
> suspect it has some way to go to be as fast as compiled Java. 
> 
> 
> I wonder what the missing  WebGL means? It never really took off did it!
> 
> Henry
> -- next part --
> A non-text attachment was scrubbed...
> Name: smime.p7s
> Type: application/pkcs7-signature
> Size: 2682 bytes
> Desc: not available

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Re: [Jmol-users] Jmol-users Digest, Vol 110, Issue 3

[Craig T Martin]

Dear all

   I am trying to take some pages created more than 5 years ago in Jmol and 
bring them up to modern JSmol/Jmol standards. I’m now using the most recent 
Jmol release, and using the Jmol2.js adapter routines. I’ve got that running 
fine with a simple test page, but have not been successful with my more complex 
pages.

  In particular, my “complex” page does a lot of javascript rendering of the 
HTML, through calls in the Header section, followed by a call at the end of the 
HTML body (this allows a common framework from my own javascript library, but 
includes simple user HTML).

  As you can see in the code below, what I would like to do is to load my Jmol 
applet into a DIV after the page/document has fully loaded. I create (not 
shown) a DIV dedicated to the applet and I do the call to jmolApplet into a 
variable. Finally, after the page has loaded, I’m trying to load that variable 
into that existing DIV. Everything is working fine, but nothing loads into the 
DIV. No error messages (though I may not know everywhere to look for those).

Any advice here? If you want to play with the page, it can be found at
http://people.chem.umass.edu/cmartin/Jmol/KissingLoopRNA/jsindex.html 
http://people.chem.umass.edu/cmartin/Jmol/KissingLoopRNA/jsindex.html

And the older, functioning (and Java-only) page at
http://people.chem.umass.edu/cmartin/Jmol/KissingLoopRNA/jsindex.html 
http://people.chem.umass.edu/cmartin/Jmol/KissingLoopRNA/jsindex.html

Thanks,

Craig Martin

// ===
//Global variable
var StoredCodeJmol;

//Writes to DIV JAppDIV, previously prepared
function AfterLoaded() {
$('#JAppDIV').html(StoredCodeJmol);
}

// Set to call above after the document is fully loaded/rendered
$(document).ready(function(){AfterLoaded()});

// Temporarily turn off direct writing
jmolSetDocument(0);

StoredCodeJmol = jmolApplet([1.0,1.0], LoadScript);

//Restore direct writing by Jmol.js calls
jmolSetDocument(document);
// ===

I do get the following in the console, if that’s helpful
=
[Log] JSmol load jmolApplet0 loadClazz... (JSmol.min.js, line 273)
[Log] JSmol load jmolApplet0 start applet... (JSmol.min.js, line 273)
[Log] JSmol exec jmolApplet0 loadClazz null -- OK (JSmol.min.js, line 272)
[Log] xhr.open async=false url=../jsmol/j2s/core/package.js (JSmol.min.js, line 
178)
[Log] xhr.open async=false url=../jsmol/j2s/core/package.js (JSmol.min.js, line 
178)
[Log] xhr.open async=false url=../jsmol/j2s/core/corejmol.z.js (JSmol.min.js, 
line 178)
[Log] xhr.open async=false url=../jsmol/j2s/java/net/UnknownServiceException.js 
(JSmol.min.js, line 178)
[Log] xhr.open async=false url=../jsmol/j2s/J/io/JmolBinary.js (JSmol.min.js, 
line 178)
[Log] xhr.open async=false url=../jsmol/j2s/J/g3d/PrecisionRenderer.js 
(JSmol.min.js, line 178)
=
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[Jmol-users] Fwd: Jmol-users Digest, Vol 90, Issue 23

[Craig T Martin]

If I might interject - code signing and the lot should be viewed as a short 
term (and poor) solution to this problem.

First, I'd like to thank Bob and all of you for moving in the javascript 
direction, away from Java. Absent in this discussion is a thread ongoing about 
the security threats posed by signed applets (one the institutional IT lawyers 
will likely not ignore). See for example
http://threatpost.com/javas-losing-security-legacy
I see the Java problem only getting worse, not better, with time.

Admitting that I have not contributed directly to Jmol development (but 
recognizing that I am a huge beneficiary), may I throw out a challenge for all 
of you very creative folk? The challenge is to fully harness GPUs in the JS 
version of Jmol - WebGL, or something of the sort. Beyond solving short term 
problems, I'm guessing it would allow us to leap frog over where we are now and 
start to do even more wondrous things with Jmol

I think I understand that maintaining cross-platform compatibility might be a 
challenge, but surely no more than the challenge that you all overcame in 
moving to JS in the first place (not that long ago, I was told it would/could 
not be done). Perhaps code could detect incompatible systems and revert to the 
current JS-only code. But if Jmol exploited the GPU on most major platforms, 
think of the opportunities!

Java is history. We need to run away fast. GPU's are where computer makers are 
focusing their efforts. Might I prompt a discussion of a solid GPU-embraced 
future for Jmol?

My deepest appreciation to all of you who have contributed so much for the rest 
of us,

Craig

Craig Martin
cmar...@chem.umass.edu


Begin forwarded message:

 Message: 4
 Date: Wed, 06 Nov 2013 10:50:19 +
 From: Dave Howorth dhowo...@mrc-lmb.cam.ac.uk
 Subject: Re: [Jmol-users] Important Java changes - January 2014
 To: jmol-users@lists.sourceforge.net
 Message-ID: 527a1eeb.6050...@mrc-lmb.cam.ac.uk
 Content-Type: text/plain; charset=UTF-8
 
 Nicolas Vervelle wrote:
 On Wed, Nov 6, 2013 at 8:11 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote:
 I think this is great for testing, but what will happen in ?production
 mode?   Inevitably when one talks to large organisations (as I did with the
 ACS and  RSC), they ask ?what will our lawyers make of it??  So could we
 issue Jmol in the name of one individual, and would that individual be
 happy potentially dealing with eg  ACS and RSC lawyers?
 
 Or, how could we set up  Jmol as an  ?organisation? so that the
 certificate goes out in its name?
 
 Maybe, but I don't know how to get a free or cheap code-signing certificate
 for an organisation, even a non-profit one.
 But, sure, that would be a better option.
 
 ...
 
 I really don't know what are the legal implications of code signing, if
 there are...
 
 It seems to me that this is the crux of the problem. To solve the
 problem, I think it will be necessary to speak to lawyer(s) who
 specialize in the area. Presumably Oracle, and perhaps the Java
 community, have access to lawyers who understand the implications of the
 plan, so it might be worth asking them. Alternatively, I think it would
 be worthwhile sending an enquiry to i...@eff.org to see whether they
 could help or suggest some other contacts. That is, unless anybody
 already has access to a suitable lawyer.
 
 BTW,
 
 So perhaps JSmol could be tuned  (along with the  JavaScript engine)
 to do the  same.  But not I fancy for a year or two?
 
 Even when/if Javascript has been tuned, not everybody will be using the
 latest version. So it will be necessary to continue support for some
 time unless it's acceptable to break those users' experience. Certainly
 it's extremely unlikely there will be a 100% upgrade to a JS-only
 solution by next January IMHO.
 
 Cheers, Dave
 

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[Jmol-users] Fwd: Jmol-users Digest, Vol 88, Issue 60

[Craig T Martin]

Dear Paul and other Jmolers,

  Yes, I would be delighted to provide the software, and any other guidance, 
for setting up your own Molecular Playground. A description of the project and 
basic installation guidelines can be found at http://molecularplayground.org. 
My goal is to have the software downloadable from that site in the future, but 
for the moment, you can request it directly from me. The programmer for the 
project has moved on (now developing iOS software for Apple), but is still 
wrapping up the final touches remotely (and alas, slowly). In the mean time, 
although I am pursuing funding sources to add new features, the software is 
stable and running well at 8 (so far!) installations.

   Full integration into Jmol could be interesting and if anyone wants to take 
that on, I'm happy to help (I don't program, myself, at least at this level). 
My goal is to take the project fully into the open source domain. 

   Installation (Mac only, sorry) is trivial. MPControlHub is the setup 
interface and launches the other components. I'll soon work on some 
documentation for that, but the program is pretty intuitive and simple. Our 
final goal is to have content hosted on a server here at UMass, transferring 
the configuration of individual installations to a simple WEB interface. At the 
moment, the files I'll send you contain a collection of content that you can 
turn on and off from within the MPControlHub application. Adding your own Jmol 
molecules and scripts, simply requires editing  a couple of configuration 
(text) files, and should be trivial for most on this list. 

And I would love to have an even wider variety of content available to 
Playgrounds. If anyone plays with the setup and new content, I'd love it if you 
would share that content with us.

Sorry for the delay in my response,

Craig Martin
cmar...@chem.umass.edu

http://MolecularPlayground.org




Begin forwarded message:

 Message: 1
 Date: Fri, 20 Sep 2013 22:24:56 -0400
 From: Paul Pillot paul.pil...@ac-orleans-tours.fr
 Subject: [Jmol-users] How to set up a molecular playground
 To: jmol-users@lists.sourceforge.net
 Message-ID: 720aa7ac-4ae0-4a7b-b9fd-41fb6a71f...@ac-orleans-tours.fr
 Content-Type: text/plain; charset=us-ascii
 
 Dear Jmolers,
 I would like to set up a Molecular playground. I have read extensively the 
 molecularplayground.orgwebsite, but I could not find any information 
 regarding the software used nor download it.
 After some googling, I've seen on Angel's dedicated webpage that MPControlHub 
 and MPJmolApp are required.
 I have found MPJmolApp in Jmol's source code.
 I have also found some references on the dev list to the moleK project that 
 does not use MPKinectDriver and seems to run on linux systems
 
 So, where should I start ? Can someone explain how the software part of the 
 setup can be done ? Plus, is a mac required to run it ?
 
 Thank you for your help,
 Paul

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Re: [Jmol-users] Jmol-users Digest, Vol 84, Issue 46

[Craig T Martin]

On May 31, 2013, at 9:49 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 3
 Date: Fri, 31 May 2013 11:35:48 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Wikis using JSMol?
 To: jmol-users@lists.sourceforge.net
   jmol-users@lists.sourceforge.net
 Message-ID:
   caf_yuvw_zdvjqcrzfyzsiwqm75mjzb9jbu-pakul8lkn7oi...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 I have a file that can be slipped in for Jmol.js that makes older pages
 work as JSmol.

Can you point us to that file? Perhaps I should know from a previous post?

Haven't yet tried this, but am looking forward to it (as you know!).

Craig

 Wouldn't that work? What does Java vs JavaScript have to do
 with the fact that it is a wiki? (unless there's a jQuery incompatibility,
 I suppose).
 
 
 
 On Fri, May 31, 2013 at 8:45 AM, Angel Herr?ez angel.herr...@uah.es wrote:
 
 
 You just flip the switch in Info from use:Java to use:HTML5.
 
 I don't think so. The existing information for Wikis will use either

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Re: [Jmol-users] Jmol-users Digest, Vol 82, Issue 80

[Craig T Martin]

Daniel

   JSmol for the following seems to be loading on my iPhone, but I'm getting 
the error:

Error reading the file at line 166
REMARK 2901555 X,Y,Z
TypeError: 'null' is not an object
for file http://biology.kenyon.edu/BM
type Pdb

-

Craig Martin

On Mar 25, 2013, at 3:24 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 2
 Date: Mon, 25 Mar 2013 15:29:19 -0400
 From: Daniel Barich bari...@kenyon.edu
 Subject: [Jmol-users] IE9 not working with my page
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   cae3pvryz1gg0vei1sw18hg2fk8gajkmyrmud80pljvgadzy...@mail.gmail.com
 Content-Type: text/plain; charset=utf-8
 
 I can't get IE9 to run JSmol on my page.  Any idea why?
 
 http://biology.kenyon.edu/BMB/biomolecules.htm
 
 Thanks.
 
 Daniel

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Re: [Jmol-users] Jmol-users Digest, Vol 82, Issue 81

[Craig T Martin]

Forgot to note that it loads fine on my Mac.

Just checked - it's also loading on my iPad (and user-rotates nicely! Thanks 
again to Bob and colleagues!)

Actually - just rechecked on my iPhone, but this time I closed a bunch of open 
pages. 
Now it loads correctly (and performs well). A memory issue?

I'm certain of the original error - even loaded it twice, with same error.

Craig

On Mar 25, 2013, at 4:13 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 1
 Date: Mon, 25 Mar 2013 15:37:22 -0700
 From: Craig T Martin ctmar...@chem.umass.edu
 Subject: Re: [Jmol-users] Jmol-users Digest, Vol 82, Issue 80
 To: jmol-users@lists.sourceforge.net
 Message-ID: 764e20ec-eb89-4c64-ba0d-4b610ca30...@chem.umass.edu
 Content-Type: text/plain; charset=us-ascii
 
 Daniel
 
   JSmol for the following seems to be loading on my iPhone, but I'm getting 
 the error:
 
 Error reading the file at line 166
 REMARK 2901555 X,Y,Z
 TypeError: 'null' is not an object
 for file http://biology.kenyon.edu/BM
 type Pdb
 
 -
 
 Craig Martin
 
 On Mar 25, 2013, at 3:24 PM, jmol-users-requ...@lists.sourceforge.net wrote:
 
 Message: 2
 Date: Mon, 25 Mar 2013 15:29:19 -0400
 From: Daniel Barich bari...@kenyon.edu
 Subject: [Jmol-users] IE9 not working with my page
 To: jmol-users@lists.sourceforge.net
 Message-ID:
  cae3pvryz1gg0vei1sw18hg2fk8gajkmyrmud80pljvgadzy...@mail.gmail.com
 Content-Type: text/plain; charset=utf-8
 
 I can't get IE9 to run JSmol on my page.  Any idea why?
 
 http://biology.kenyon.edu/BMB/biomolecules.htm
 
 Thanks.
 
 Daniel

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Re: [Jmol-users] Jmol-users Digest, Vol 74, Issue 43

[Craig T Martin]

Confirmed on my Mac with Mountain Lion, despite the relaxation of security 
noted below

And yes, no problems with Chrome or FireFox - only Safari 6

Error message is:
You do not have Java applets enabled in your web browser, or your browser is 
blocking this applet.
Check the warning message from your browser and/or enable Java applets in
your web browser preferences, or install the Java Runtime Environment from 
www.java.com

But of course, Java is enabled. Works fine connecting to the exact same site, 
networked.

Craig Martin
ctmar...@chem.umass.edu



On Jul 31, 2012, at 1:43 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 3
 Date: Tue, 31 Jul 2012 08:15:49 +0100
 From: Rzepa Henry h.rz...@imperial.ac.uk
 Subject: Re: [Jmol-users] Signed applet v Mountain Lion
 To: jmol-users@lists.sourceforge.net
 Message-ID: 7c60735c-10b5-4cf7-8f86-941f749fe...@imperial.ac.uk
 Content-Type: text/plain; charset=us-ascii
 
 
 On 26 Jul 2012, at 11:32, Greeves, Nick ngree...@liverpool.ac.uk wrote:
 
 If you try Mountain Lion and sites with the signed applet you may find you 
 are unable to enable the applet.
 It is new security feature in Mac OS X, by default only apps from Mac Store 
  from trusted developers are allowed to run there. Fortunatelly, it is easy 
 to change, you have to allow this in Mac OS X preferences.
 
 Go to Preferences - Security  Privacy and click on padlock to allow 
 changes.
 
 Then in Allow appications downloaded from select Anywhere.
 
 After that, the button in Java dialog will be enabled.
 
 
 Can anyone reproduce this?  Although doing the above allows OS X Mountain 
 lion to run signed Jmol from a remote server, trying to run the same from a 
 local hard drive produces the message You do not have Java applets enabled 
 in your web browser, or your browser is blocking this applet (which comes 
 from jmol.js).  I have tried this on two quite separate  Mountain Lion 
 installs with the same result.
 
 However, it is specific  to Safari; Chrome and  Firefox are fine on the same 
 systems (i.e. Java is present). 

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[Jmol-users] Jmol/ChemDoodle

[Craig T Martin]

Bob and Kevin

   The page DOES work for me using Safari on a Mac (Lion 10.7.3 with 
yesterday's Java update). It also DOES work with FireFox and Chrome (latest of 
both).

   UPDATE --- Just read the next digest (came while I was writing). Yes, I do 
have the Dev Tools showing and do have WebGL enabled (don't remember why I did 
that). And yes, disabling WebGL kills it in Safari (but it nicely tells you 
that your browser does not support WebGL). Maybe my report here is already 
obsolete, but I'll send this along anyway.

In any case, in all three browsers, everything seems to work.

Craig Martin


 Message: 2
 Date: Fri, 6 Apr 2012 14:20:12 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: [Jmol-users] Jmol/ChemDoodle
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   caf_yuvvdkaafrxcqqqj604tbp_jsxhuylvcrjkvvznhqplt...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Kevin, I'm experimenting some with hybridizing Jmol and ChemDoodle. But I'm
 having problems just getting ChemDoodle to work at all.
 
 Can you tell us what the specific browser requirements (working versions)
 are for http://web.chemdoodle.com/demos/molgrabber-3d
 (I've seen http://web.chemdoodle.com/installation/browser-compatibility but
 what it says there is not my experience.)
 
 What browsers really do support WebGL?
 
 On my Windows laptop I couldn't get MSIE 9, Firefox 11 (fresh
 installation), or Opera 11 to show anything on that page but a big black
 rectangle telling me that I don't have WebGL. Only Chrome worked (thank
 you, Jonathan!). Nor could I get that to show anything on my iPhone running
 whatever that runs. (Safari, I imagine.)
 
 Are other Jmol users more successful seeing a molecule on that page?
 
 Any ideas when ChemDoodle is going to be more generally available?
 Is WebGL really
 Bob
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry


Craig Martin
cmar...@chem.umass.edu



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Re: [Jmol-users] Jmol for iPads?

[Craig T Martin]

Looking at my comment below out of context, I feel a need to clarify. I am 
EXTREMELY thankful to the dedicated core who have put so much into the 
development of Jmol. I have benefitted greatly from the selfless efforts of 
others.  I am also very aware that my request to move Jmol away from Java and 
to HTML5/OpenGL is not at all trivial. If no one wants to take this on, I will 
fully understand, and I regret that I do not have the skills to take this on 
myself. So please don't take this as a demand, but rather as a 
request/suggestion... As a user, I see this as the next big challenge for Jmol, 
but I appreciate that it is both big and a challenge.

Craig Martin

 Message: 2
 Date: Fri, 30 Mar 2012 08:53:35 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Jmol for iPads?
 
 Absolutely.
 
 On Fri, Mar 30, 2012 at 8:01 AM, Craig T Martin cmar...@chem.umass.eduwrote:
 
 The challenge of open source is who's going to fix this and how? Perhaps
 our discussion should move in that direction?
 
 -- 
 Robert M. Hanson
 Professor of Chemistry


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Re: [Jmol-users] Jmol for iPads?

[Craig T Martin]

Wow. I've stepped into (and probably added fuel to) a firestorm.

I'd like to suggest that this is not the forum for arguing the merits of iOS vs 
Android. Some of us are a bit fanatical about iOS (OK, I'm one of them), and 
some fanatical about Android. But we're all unified in being fanatical about 
Jmol.

I think we can all agree that Jmol should be accessible to as many people on as 
many platforms as possible. In the days of CHIME, one could write a WEB page 
that included glorious interactive content, but users who did not install the 
plug-in (or who were using newer cutting edge browsers, if I remember 
correctly) were met with an error message. Jmol's biggest advancement (among a 
huge list of advancements) was fixing that glaring problem. I can write a WEB 
page with embedded molecules and be assured that every user sees what I want.

Alas, we're now revisiting history. One can argue that this is all Apple's 
fault for not supporting Java, but that won't change reality. We can't simply 
tell users the equivalent of well, just stay with Netscape 4.x and everything 
will be fine. They will use what they use - and we want to reach them all. And 
as with CHIME, authors will be less inclined to use Jmol if they know that 
there are significant markets that cannot be reached.

So yes, Jmol should run on Android, and yes, it should run on iOS, regardless 
of where one stands in the platform war... The challenge of open source is 
who's going to fix this and how? Perhaps our discussion should move in that 
direction?

Thanks to everyone for their passions - that's what keeps Jmol dynamic!!

Craig Martin
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[Jmol-users] Multiple, discontinuous models

[Craig T Martin]

Greetings,

   I've aligned a good number of different structures of T7 RNA polymerase at 
various stages of transcription and then set them all as individual models in 
one file. Thus, when I select an active site residue for example, and color it, 
it applies across models. I can then set up a radio button panel to look at 
each structure, identically arranged.

Quick question:

I'd rather use a Checkbox set and be able to overlay multiple models. With the 
Model/Frame command, I can show consecutive models (Model 1-2), but I cannot 
show random groups (Model 2, 4, 8). Is there a way to do this? I know how to do 
the Javascripting - it's the Jmol command I'm looking for.

Display/hide seems not to be able to apply to Models (intentionally, I guess)

This in Jmol 11.8.24.

Thanks,

Craig Martin
ctmar...@chem.umass.edu




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Re: [Jmol-users] Jmol-users Digest, Vol 19, Issue 21

[Craig T Martin]

While we're talking memory allocation, and with respect to:

And unfortunately the memory of applets whose window/tab was closed  
it not always release 


For the stuff that I'm doing, I've known for some time that after  
loading (and closing) various windows, Jmol eventually stops working  
(Jmol, not the browser, hangs on a subsequent load) and I have to  
restart the browser. This on a Mac running either Safari or FireFox  
(latest everything, but it's been happening for more than a year). If  
I look at the memory allocated to Safari, for example, I can see a  
step increase on every new Jmol applet. So it is clearly not  
releasing memory.


I think I've seen this discussed here before, but with no real  
answer. Is there a way to insure that when an applet closes, it  
releases its memory? Or is there a way to manually do so? Is this  
just a problem for me or do others see this? Perhaps I'm doing some  
sort of call wrong?


An implementation is at:
http://www.chem.umass.edu/people/cmartin/Jmol/WingedHelixII

You need to open and close maybe a half dozen times to see the effect.

Thanks,

Craig

On Dec 13, 2007, at 9:43 AM, [EMAIL PROTECTED]  
wrote:



Message: 3
Date: Thu, 13 Dec 2007 14:56:34 +0100
From: Rolf Huehne [EMAIL PROTECTED]
Subject: Re: [Jmol-users] Exploring the limits

Timothy Driscoll wrote:

On Dec 13, 2007, at 6:28 AM, Rolf Huehne wrote:

Because an OUT OF MEMORY error freezes Jmol and the standard user
most

...


The problem with this is that there is no standard java memory
allocation. In my experience it differs largely between operating
systems and also between Java versions.

Another problem is that even if you could apply some rule of thumb
(e.g.: 20 times uncompressed file size + minimum requirement for the
applet) this would only apply if a single applet was started.
But I would rather expect that often a user will explore several
structures one after the other. And unfortunately the memory of  
applets

whose window/tab was closed it not always released.

Another problem is the applet size. Since the user can set the size
freely this might also drastically change the memory required.

So I would really prefer a more situation-specific solution.

Regards,
Rolf


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Re: [Jmol-users] Jmol-users Digest, Vol 19, Issue 21

[Craig T Martin]

While we're talking memory allocation, and with respect to:

And unfortunately the memory of applets whose window/tab was  
closed it not always release 


For the stuff that I'm doing, I've known for some time that after  
loading (and closing) various windows, Jmol eventually stops  
working (Jmol, not the browser, hangs on a subsequent load) and I  
have to restart the browser. This on a Mac running either Safari or  
FireFox (latest everything, but it's been happening for more than a  
year). If I look at the memory allocated to Safari, for example, I  
can see a step increase on every new Jmol applet. So it is clearly  
not releasing memory.



Sorry for the addendum - to be clear, simply reloading the page for  
the same applet leads to the stepwise increase in browser memory.  
Does NOT require multiple applets.


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Re: [Jmol-users] new.htm updated

[Craig T Martin]

Message: 1
Date: Wed, 28 Nov 2007 08:44:30 +
From: David Leader [EMAIL PROTECTED]
Subject: Re: [Jmol-users] new.htm updated
To: jmol-users@lists.sourceforge.net
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Bob wrote:



I've updated

http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

with the very latest for Jmol. Most notably:



But on Mac 10.4.11 the applet on the page does not load using either
Safari or Firefox (both latest versions) The Sun Java wait thingy
just keeps going round with the progress bar about a quarter of the
way along or less.

No error messages in the console to give any clue what the problem is.

My own jmol applets - somewhat older vintage - work ok.

David


I can confirm that everything works fine on both my (Intel) Mac  
running 10.4.11 and

on my (G4) Mac running 10.5.1

Craig

Craig Martin
[EMAIL PROTECTED]



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[Jmol-users] Developing a Jmol test bed

[Craig T Martin]

Greetings (again, already)

   I've just found a fix for the problem I posted yesterday.

I am trying to develop a WEB page that will display a Jmol  
image and then have two sections along the side. In one section,  
the user can enter full HTML text into a form field, including  
Jmol.js calls (such as 'jmolButton'). The other panel can then load  
the code from the form field into the .innerHTML of the second  
section (a DIV). The goal is to let people test out code snippets  
before moving them into their final HTML files.


   The transfer from the form field to the DIV.innerHTML is working  
well and code such as bdog/b correctly displays the word 'dog'  
in bold. All HTML code is properly interpreted. However, when I  
include scriptjmolButton(..,..)/script, everything from the  
opening script tag to the closing script tag is simply ignored.  
Other HTML code past that point displays correctly.


   I'm guessing that I may be trying to do something that browsers  
don't allow - a security issue perhaps? Does anyone have any  
workarounds?




   The solution is made possible by the genius and insight of the  
Jmol developers. I process the text, pulling things within SCRIPT  
tags and then use the eval function in Javascript. I have been  
using Jmol.js in the write directly to document mode, but just before  
eval I set jmolSetDocument(false) (and then reset it on).


   It's working great now. Thanks to the foresight of all of the  
Jmol developers!



   To see what I have so far and test it out, go to:


   http://people.chem.umass.edu/cmartin/Jmol/WingedHelixII

  Then click on 'Cmd' at the top and look down to 'Test Bed' and  
'Preview'


  This allows authors of presentations to test out their HTML code  
in real time, without having to refresh the browser window. This  
aspect, I suspect, may be of more general interest. I welcome comments.


Thanks,

Craig Martin
[EMAIL PROTECTED]



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[Jmol-users] Developing a Jmol test bed

[Craig T Martin]

Greetings,

I am trying to develop a WEB page that will display a Jmol image  
and then have two sections along the side. In one section, the user  
can enter full HTML text into a form field, including Jmol.js calls  
(such as 'jmolButton'). The other panel can then load the code from  
the form field into the .innerHTML of the second section (a DIV). The  
goal is to let people test out code snippets before moving them into  
their final HTML files.


   The transfer from the form field to the DIV.innerHTML is working  
well and code such as bdog/b correctly displays the word 'dog' in  
bold. All HTML code is properly interpreted. However, when I include  
scriptjmolButton(..,..)/script, everything from the opening  
script tag to the closing script tag is simply ignored. Other HTML  
code past that point displays correctly.


   I'm guessing that I may be trying to do something that browsers  
don't allow - a security issue perhaps? Does anyone have any  
workarounds?


   To see what I have so far and test it out, go to:
   http://people.chem.umass.edu/cmartin/Jmol/WingedHelixII

  Then click on 'Cmd' at the top and look down to 'Test Bed' and  
'Preview'


Thanks,

Craig Martin
[EMAIL PROTECTED]



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[Jmol-users] Models and Monitor

[Craig T Martin]

Greetings,

  I have a question regarding viewing different models of a protein.  
If I have file containing multiple models of the same protein, I can  
issue commands to select and color different regions, for example,  
and those commands works across all models.


  If I issue a monitor command, that appears to apply only to the  
current model.


  Is this a bug or a feature?  How can I issue a monitor command  
that crosses models?


Thanks,

Craig Martin
[EMAIL PROTECTED]



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[Jmol-users] Re: Jmol-users digest, Vol 1 #993 - 11 msgs

[Craig T Martin]

Very cool. Works fine on my system-up-to-date Mac.An issue though. At least in your current implementation, with sync "on" all align to the same intrinsic reference frame. That's desirable for some situations. However, if I have for example coords for A-form and D-form DNA, I'll want to independently set their views (with, for example, the central major groove facing the user) and then turn on a "relatively" sync'ed rotation. As you have it, if the structures don't start out with major grooves oriented similarly (from their coord files), then sync'ing will put them "out of sync." Did I muddle that?I do realize that I could first align them in another program and then spit out aligned coordinates, but...Thanks for all of the recent innovation!  Amazing and appreciated. At the moment, I'm too swamped with other things to do anything but watch from the sidelines, but when I get time again, I'll enjoy playing with the wealth of new options.Craig Craig Martin[EMAIL PROTECTED] On Mar 9, 2006, at 2:11 PM, [EMAIL PROTECTED] wrote:Message: 9 Date: Thu, 09 Mar 2006 12:48:05 -0600 From: Bob Hanson [EMAIL PROTECTED] To: jmol-developers@lists.sourceforge.net, jmol-users@lists.sourceforge.net Subject: [Jmol-users] applet synchronization test #2 Reply-To: jmol-users@lists.sourceforge.net  OK, a new idea for applet synchronization. Please tell me if it works:  http://www.stolaf.edu/people/hansonr/jmol/test/json/sync.htm  It's not fully articulated, but the basic idea being tested here is direct applet-applet communication via a static appletRegistry 

[Jmol-users] Re: Jmol-users digest, Vol 1 #970 - 5 msgs

[Craig T Martin]

On Feb 15, 2006, at 11:30 PM, jmol-users- 
[EMAIL PROTECTED] wrote:



Message: 3
Date: Wed, 15 Feb 2006 18:01:57 -0600
From: Bob Hanson [EMAIL PROTECTED]
Subject: Re: [Jmol-users] applet -- callback brainstorming

.




It's certainly an interesting challenge -- the goal, to provide a
snapshot of the state of the system. There are two logical
approaches I can think of:

a) a record of scripts run.
b) a dump of properties for every single atom, preferably grouped into
sets.


I see this as TWO SEPARATE issues.

1) A save state question. Just as we can leave any drawing program  
and come back to a saved state, it makes sense that one would want  
that kind of ability in Jmol as the program matures. The under-the- 
hood details may be ugly and don't need to be edited/accessed by  
mere mortals such as myself.


2) Script recorder - the script recorder in PE is, I think, most  
useful for troubleshooting/building one's own scripts. One would like  
to be able to turn the recorder on and off, and clear it at times to  
start fressh. This is better for recording a relatively small (100?)  
number of user events.


For perspective, I'm thrilled that we're now getting greedy with next- 
level requests. The progress to date on Jmol has been fantastic!  
Thanks to Miguel and all who contribute development time!


Craig Martin
[EMAIL PROTECTED]


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[Jmol-users] Re: Jmol-users digest, Vol 1 #962 - 7 msgs

[Craig T Martin]

On Feb 9, 2006, at 11:33 PM, [EMAIL PROTECTED] wrote:Message: 4 Date: Thu, 09 Feb 2006 13:07:47 -0600 From: Bob Hanson [EMAIL PROTECTED] To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] applet -- callback brainstorming Reply-To: jmol-users@lists.sourceforge.net  I'm looking at the Jmol callback issue. - - - - - -   AS A USER, WHAT DO YOU WANT?  a) Do you implement callbacks? If so, which ones?Yes, I use pickCallback and messageCallback  b) What WOULD you use if you had it available?Oooh. One never knows... I'm already thinking that information on user rotation/zoom might be used to make a second window mimic a first window. ie., the user rotates one frame and the other follows. Side-by-side comparison of things like B vs A vs Z form DNA, for example.  c) What sort of information (exactly) are you looking for?User picks, for sure. I've used it to provide a nicer interface for identifying residues picked.  d) Is there a particular format that you would like to see,     other than just the current text-stream of messages?I like your structured variable approach. Much easier to deal with.  e) Is it important to you that this mechanism be backward     compatible?Oh, I guess not...  MORE SPECIFC QUESTION:  1. There are currently four callbacks:  animFrameCallback loadStructCallback pickCallback messageCallback  Each of these fulfills an obvious need. Should there be more "callback-like" options? If so, what? If you build it, they will codeCraig Martin

[Jmol-users] Re: Jmol-users digest, Vol 1 #963 - 9 msgs

[Craig T Martin]

On Feb 10, 2006, at 1:58 PM, [EMAIL PROTECTED] wrote:I don't see a difference whether I say  monitor 2087 2088 or monitor ([LIP]3:A.O5) ([LIP]3:A.O6)  Oh, sure. OK. I don't know that we are headed that way wth the monitor  command, because there are some programming issues with putting two atom  expressions in the same command -- nothing really insurmountable,  really, but not exactly trivial.I appreciate the non-triviality, but it would be IMMENSELY useful!I have the same protein, in various crystal forms, with/without ligand, etc.   It's hard to write a monitor script that works the same on all of them, since the atomno's are all different...  I would LOVE this feature!CraigCraig Martin[EMAIL PROTECTED] 

[Jmol-users] CHIME2Jmol

[Craig T Martin]

Folks,For those of you trying to convert from CHIME to Jmol, I offer the following modest resource:    http://www.chem.umass.edu/people/cmartin/Jmol/Development/CHIME2Jmol.htmlIt presents a simple form that takes HTML code containing CHIME instructions and tries to convert them to equivalent Jmol instructions (assumes the use of Jmol.js routines in your final page). Paste your code into input, press "Convert" and then copy the result from output.This is by no means complete, but does a surprisingly good job for the basics of buttons, links and toggles. Definition of the applet window will still have to be done by hand.If anyone wants to augment it's capabilities, feel free (but I'd love to hear about it!) Craig MartinDept of ChemistryUniv of Massachusetts at Amherst[EMAIL PROTECTED] 

[Jmol-users] Update Request for Monitor / Measure command

[Craig T Martin]

In the category of wish lists, may I propose the following?

Currently monitor (measure) uses AtomNo for each of its parameters.

As I develop a single page to service an Applet that can dynamically  
load different, related structures,
the monitor command, of course, is less useful.   The S on  
Cys35, chain B has different atom numbers
in the two structures. Most of my other commands work fine in  
this context.


Might I suggest that the Monitor/Measure algorithm optionally take a  
unique atom descriptor for each of its arguments?


Example: monitor 184:A.CA 367:A.CA

Thanks,

Craig Martin
[EMAIL PROTECTED]





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Re: [Jmol-users] demonstration page for new capabilities of Jmol.js

[Craig T Martin]

First, a big thanks to Bob for his tip on including MessageCallBack.   
It's working great.


--

Regarding the message header above, I have a project I'm working on  
that needs to be run both locally and from the WEB. I'd like to  
include the ability to load a remote structure, as you suggest, but  
its peripheral to the project and I want my code to detect whether  
the person can actually access his code (ie., they might be offline)  
and omit the option in that case.


What is the easiest way for my code to detect whether or not his  
remote JavaScript has run successfully?




Third issue: several have complained about various things on the Mac  
not working. I'm using release 10.00.39 on a Mac w/ OS 10.4.2 (all  
the updates as of today), and both Safari 2.0.1 and FireFox 1.0.7.  
Both work just fine with everything. I'll guess that the most recent  
Mozilla also works fine, but I don't test it often.


Craig

Craig Martin
[EMAIL PROTECTED]





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Re: [Jmol-users] detecting offline activity

[Craig T Martin]

Date: Wed, 28 Sep 2005 09:35:43 -0500
From: Bob Hanson [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] detecting offline activity
Reply-To: jmol-users@lists.sourceforge.net

An interesting question! Right, now that you can have a page local and
still access anything online, the question becomes -- how do you know
if you are local! I pulled the plug on my machine to see what would
happen with these script node calls. The answer is: nothing. No error,





ALternatively, if you want to check to see if a machine is totally
offline right when the page loads, the following might work:


Yes, the key question is: can the user access your site? If not, then  
don't bother drawing a button telling them that they can access  
it...  So in particular, I want to know if they can access YOUR code  
and site, though I guess it shouldn't really matter...



a) write a little file checkonline.js that contains only:

online=true

b) place it on your website at http://somewhere/checkonlin.js

c) add the following script to your web page:


script type=text/javascript
  isonline=false
  s=''+'script type=text/javascript'
  +' src=http://somewhere/checkonline.js?'
  +Math.random()+'/'+'script'
  document.write(s)
/script
script type=text/javascript
  if(!isonline)
/script

The idea here is to load a script that changes a variable to be TRUE.
If the script doesn't load, because you are offline, then you find
that out, because the variable never gets set. The nonsense there with
the script writing another script is to ensure that no caching occurs.


Thanks - I'll play with this when I have a chance, but I don't want  
to add still more embedded Javascript calls in the top document. If I  
had my drothers, I'd have just one. Trying to keep that as simple as  
possible and keep all of the ugly stuff in my JmolShell.js


If I test for one of the internal variables in your code (or one that  
you set), I guess I'll still have a problem with cache'd code? Does  
that cache persist through browser restarts?



Bob



Third issue: several have complained about various things on the Mac
not working. I'm using release 10.00.39 on a Mac w/ OS 10.4.2  
(all  the

updates as of today), and both Safari 2.0.1 and FireFox 1.0.7.  Both
work just fine with everything. I'll guess that the most recent   
Mozilla

also works fine, but I don't test it often.



Does this include the pop-up example windows (from the selection box)
in the documentation?

http://www.stolaf.edu/people/hansonr/jmol/docs


Works in FireFox, not in Safari   ;(

In Safari, the Window pops up with the Disclaimer link, but nothing  
else.


or, if not,

http://www.stolaf.edu/people/hansonr/jmol/docs?useobject


Ditto above...

Craig



Craig Martin
[EMAIL PROTECTED]





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Re: [Jmol-users] Jmol.js -- jmolinitialize useSignedApplet

[Craig T Martin]

Message: 2Date: Wed, 7 Sep 2005 17:00:57 -0400 (EDT)Subject: Re: [Jmol-users] Jmol.js  --  jmolinitialize   useSignedAppletFrom: "Miguel" [EMAIL PROTECTED]It appears that Jmol.js can load either of the signed or unsignedapplets, as controled by jmolInitialize().1) I'm trying to use the "useSignedApplet"  feature. If I pass "" (ornothing), then it defaults to the unsigned applet.Correct.     But when I try to pass "true", I get problems loading at all.I'm sorry that I can't figure out the errors in detail - _javascript_=21 ...My apologies. This was MY mistake. Going against the rules, I had re-written one of the Jmol.js routines (added two lines - see below), but had not kept it up with newer releases of Jmol. My mistake - now fixed. SignedApplet is now chosen when told to.2) Might I suggest that the default be "automatic" and then have thecode check to see if the document is coming from a server or from thelocal file structure (using "document.location.host" or somethingmore clever to see where Jmol.js is?). If local, use the signedapplet. If not, then used the unsigned applet. This would make mylife going back and forth much easier.The purpose of the signed applet is not to allow one to develop againstfile://If you are building pages for deployment on a web server then I stronglyrecommend that you do your local development against the local fileserver.My purpose is to have students in my class use Jmol to prepare a presentation which will later be posted on the WEB for other students to see. My students range in the level of their computer experience, but are generally all NOT programmers. I give them just a few function calls that I have built on top of (the wonderful) Jmol.js. Since most don't have access to a server (or understand the subtlties of running one on "localhost"), it is best for them to use local files with the signed applet during development.3) Finally, and minor, my reading of an error message is that theparameters for jmolInitialize should be "codebase, badbrowserURL, and=Correct.That error message is out of date.browser check parameters are now handled by  function jmolCheckBrowser(action, urlOrMessage, nowOrLater)Thanks for the quick fix!MiguelNew, but related, request:The reason that I had to hack a routine in Jmol.js is because I wanted to include MessageCallBack and PickCallBack in my application. Is it possible to add two optional parameters to the jmolApplet function, to allow specification of these routines? Craig T Martin[EMAIL PROTECTED] 

Re: [Jmol-users] decimal places in measurements

[Craig T Martin]

I must weigh in here. I'll be surprised if the hundredths place has reasonable significance in any protein crystal structure. Indeed, the tenths decimal place is likely weak in many structures. Remember also that in a distance measurement the uncertainty doubles.We do a disservice to the novice user to present distances to 3 decimal places (OK, even to many non-novice users). It gives them an improper sense of the data. I would prefer a default of 1 decimal place for Angstroms.If a user selects 3 decimal places, an alert should pop up asking them if they know what they're doing   ;)Craig MartinP.S.  does anyone really believe that gas pumps can measure your purchase to 0.001 gallons (0.8 tsp; 4 mL)?From: Frieda Reichsman [EMAIL PROTECTED]Subject: Re: [Jmol-users] decimal places in measurementsDate: Tue, 30 Aug 2005 10:25:06 -0400Is there a way to limit the number of decimal places shown next tomonitor lines? I would like only one (can't find this documented, ifitis please let me know).On Aug 28, 2005, at 10:50 PM, Miguel wrote:There is currently no mechanism to support this.If this is not too difficult to implement, I would find it very usefulto be able to round off the decimals to one place. In cases where youare indicating several nearby measurements in one structure, they windup obscuring the structure itself. In addition, at least for angstromsI think the additional decimal places may not be significant. Any hopefor this feature request?Frieda

Re: [Jmol-users] The woes of big molecules

[Craig T. Martin]

Whoops! Don't know where I got *X as a chain identifier, but it's been 
working for me (until now) for years! I will switch the proper syntax!

Craig
--On March 21, 2005 5:25:42 PM -0500 Eric Martz [EMAIL PROTECTED] 
wrote:

Hi, Craig,
The Chime syntax for selecting chain 4 is select :4, not select *4.
The former works. The latter (in Chime -- I haven't tried jmol) selects
all residues numbered 4 but not chain 4.
While on the subject of digits in names, the Chime syntax for selecting a
group name that includes digits is select [so3]. select so3 doesn't
work! This is because the default interpretation is that the group name
is letters and the first digit begins a sequence number, as in select
asp226. (Recall that group names can be 1-3 letters, e.g. a and ca.)
I have a close to comprehensive intro to select commands in RasMol and
Chime at
http://www.umass.edu/microbio/rasmol/seleccmd.htm
Worse than digit-named chains, some PDB files have so many chains that
both upper and lower case letters are used for different chains, and also
punctuation. Chime can't handle the case distinction, nor the
punctuation. So, count yourself lucky with only 32 chains in 1KQS!
Then there are the cases of 2-letter names aligned in the PDB file's
3-character field so that Chime can't handle them, such as ca  vs. 
ca!
Good luck, -Eric
At 3/21/05, you wrote:
Greetings,
 I've run across another issue arising from my trying to set up some
Ribosome pages (I'm still struggling with memory issues on Mac browsers).
 It turns out that there are more chains in the structure 1KQS (and some
other ribosome structures) than there are letters in the alphabet. So in
addition to the letters A-Z, the authors have used 0, 1, 2, 3, and 4 as
chain identifiers.
 However, when I issue the command select *4, I select all residues
numbered 4 in all chains. What are the rules about this, either within
the PDB or in Jmol/CHIME? Can chains have numeric designators and if so,
how does one select them?
 Clearly, we can't ask the ribosome to consolidate   ;)
Thanks,
Craig
Craig Martin
Univ of Mass
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Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
Biochem Structure Tutorials http://MolviZ.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
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   http://www.umass.edu/molvis/martz
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Craig Martin
Univ of Mass
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[Jmol-users] Memory problems with Safari

[Craig T. Martin]

Greetings,
 I've been looking at the ribosome structures and am having trouble with 
memory limit issues in Safari on the Mac (latest updates for everything). I 
have not been hitting this limit with Mozilla on the Mac (don't know about 
others). Specifically, I can load the molecule once, but reloading the 
page, or loading another similarly large molecule leads to an out of memory 
error that can only be fixed by quitting and relaunching Safari. Is this a 
bug on Apple's part, or can the Jmol development folks get around this?

This can be seen at:
  http://copper.chem.umass.edu/~cmartin/JmolShell/Ribosome/1q82.html
As an aside, on an unrelated issue of referencing DIV's to make them 
visible or hidden, Safari is behaving as I desire, but Mozilla and Camino 
are not. Anyone have ideas there? The code that is likely at fault is in 
the function ShowDiv below:

// Figure out which browser is running
var nn4 = (document.layers) ? true : false
var ie = (document.all) ? true : false
var dom = (document.getElementById  !document.all) ? true : false
// Used to reference dHTML elements browser-specifically
function browser(id) {
 if (nn4)   { path = document.layers[id] }
 else if (ie)   { path = document.all[id] }
 else   { path = document.getElementById(id) } ;
 return path
}
// Toggle content in the JmolShell side-bar
// The following assumes multiple overlapping DIV's containing content
// on the left side. It allows toggling visibility so that only
// one is showing at a time
function ShowDiv(id)
{ browser(Main).style.visibility=Hidden;
 browser(About).style.visibility=Hidden;
 browser(Cmd).style.visibility=Hidden;
 browser(Presets).style.visibility=Hidden;
 browser(Help).style.visibility=Hidden;
 browser(id).style.visibility=Visible;
}
thanks,
Craig Martin

Craig Martin
Univ of Mass
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Re: [Jmol-users] Maximum Zoom?

[Craig T. Martin]

For my current needs, bumping the zoom up another 5X from whatever it is 
currently would probably suffice, but others might need more. At the 
moment, the ribosome is the biggest structure I've looked at, but of course 
with progress, that will change.

thanks,
Craig
Message: 9
Date: Wed, 9 Mar 2005 17:42:07 -0500 (EST)
Subject: Re: [Jmol-users] Maximum Zoom?
From: Miguel [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net
Reply-To: jmol-users@lists.sourceforge.net

Greetings,
I think I remember reading something recently regarding maximum zoom, b=
ut
I
can't find it. My question is: what sets that limit?
Uhh ... I set that limit :-)
Can the limit be increased?
It was increased recently.
The problem is this ... there is a point at which things *will* break. If=
the numbers get too big then there will be overflow/underflow/wraparound
when we try to take a huge number and try to turn it into a screen
coordinate.
I will take another look and see if I can put in some error checking to
detect this case.
I think there *needs* to be some upper limit ...
Q: How much zoom do you want? 1,000x? 10,000x ?
Miguel
Craig Martin
Univ of Mass
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[Jmol-users] Re: Jmol-users digest, Vol 1 #596 - 6 msgs

[Craig T. Martin]

Bob,
 The need to dynamically size is one of the reasons that my JmolShell page 
is written mostly on the fly via Javascript. But my implementation isn't 
perfect in that the box is sometimes a bit too big or too small, depending 
on the browser. If anyone has tips on this Javascript issue, I'm all ears.

 I also dynamically size the Applet to fill the window, since for my 
application, bigger is better. I'm not sure why there is a recommendation 
that Applets be fixed sizes. In some cases, it makes sense, but for me 
there are times when I want my applet big (to do a screen capture, for 
example) and times when I want it smaller (to allow for multiple windows, 
etc).

 At any rate, if everything is written from Javascript, then you can size 
as you like...

Craig Martin
http://www.chem.umass.edu/~cmartin/JmolShell
--On March 4, 2005 7:59:32 AM -0800 
[EMAIL PROTECTED] wrote:

Message: 4
Date: Fri, 04 Mar 2005 07:15:43 -0600
From: Bob Hanson [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net,
Chem Web Developers [EMAIL PROTECTED]
Subject: Re: [Jmol-users] Re: use of frames
Reply-To: jmol-users@lists.sourceforge.net
Frames: Pretty close! I'm almost sold on divs and ready to say I'm done
developing with frames. Can you dynamically set the height of that div
so that it adjusts to overall window height? On my machine the scroller
goes down below the bottom of my screen, so I have to scroll to scroll
That, of course, doesn't happen with frames.
Frames were so nice because they allowed for automatic fractional window
amounts. Is this possible easily with divs, or do you have to hard code
all the coordinates. position:absolute can be difficult.
[I know this is a bit off the focus of the Jmol list, so I'm
cross-posting to ChemWebDev.]
Bob Hanson

Craig Martin
Univ of Mass
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[Jmol-users] Jmol-users digest, Vol 1 #591 - 9 msgs (fwd)

[Craig T. Martin]

Angel,
 I'll keep this short, as I've posted before, but you might want to look 
at:

http://www.chem.umass.edu/~cmartin/JmolShell
This is a project originally done in CHIME with frames, now done in Jmol 
with SPAN etc. It provides pretty much the same functionality I used to 
have with frames.

Craig Martin
 Forwarded Message 
Date: March 1, 2005 8:15:40 PM -0800
From: [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net
Subject: Jmol-users digest, Vol 1 #591 - 9 msgs
Message: 7
From: Angel Herraez [EMAIL PROTECTED]
Organization: =?ISO-8859-1?Q?Universidad_de_Alcal=E1?=
To: jmol-users@lists.sourceforge.net
Date: Tue, 01 Mar 2005 18:18:09 +0100
Subject: [Jmol-users] Re: use of frames
Reply-To: jmol-users@lists.sourceforge.net
Thanks to all for your prompt replies.
Tim, I wasn't referencing the applet since I am using Jmol.js, as Bob
has commented.
Bob, thanks for your extensive and very helpful reply; I know it can
be done with tables, but I didn't want to, since I like to have a
scrollable text and a common, static model.  I hear everywhere that
frames are going away, but I still haven't found something that does
what you get so easily with frames. Today I have tried to do it with
DIVs, but I have gone half-mad wih it.
I already thought that it could have to do with the use of different
frames but it was working perfectly with the model in the left-side
frame (in fact, a couple of days ago I have ported a whole set of
pages using Eric's 2-frame template from Chime to Jmol).
Reading Bob,  I guess the looking for frames routine is finding the
applet in the first frame but not in the second one. I will try to
use Bob's suggested tweak.
For the record, Miguel, I tested with Firefox 1.0 and IE6.0, both in
WinXPpro-sp2. They behave the same (I mean just for this ;-).
Thanks again. I will let  you know about my progress.
-- End Forwarded Message --

Craig Martin
Univ of Mass
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[Jmol-users] JmolShell - A simple shell for Jmol presentations

[Craig T. Martin]

First, thanks to Miguel for his help in getting my JmolShell package 
together. Briefly, this package is for use by students in a Biomolecular 
Structure course in the preparation of Jmol-based presentations on their 
favorite protein. It is trying to be as user-friendly as possible without 
requiring the students to know much HTML or JavaScript programming. I want 
them to focus on the science.

A work in progress demo can be seen at:
 http://www.chem.umass.edu/~cmartin/JmolShell/WingedHelixII
and I welcome feedback.
For those of you who have seen this previously, I re-wrote it to avoid the 
use of frames. That was causing problems with invoking the Jmol.js library 
routines. Since it is now fancier, it breaks in old browsers. Any tips on 
detecting when I will and will not have problems and alerting the user as 
such?

It works fine in Safari on my Mac (after the Developer upgrade of Java). 
Seems to work fine on the one PC I have tested it on.

Question for the next phase:
How can I get information from the Java applet using JavaScript? 
Specifically, I'd like to put up a window that parses Jmol replies from 
user actions: id'ing atoms, getting distances, etc.?

I see from the following link:
  http://www.rgagnon.com/javadetails/java-0171.html
that it is technically possible to get Java variables from JavaScript. Are 
there hooks in Jmol right now?

Craig Martin
Chemistry, LGRT 701   545-3299
http://www.chem.umass.edu/~cmartin 

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Re: [Jmol-users] JmolShell - A simple shell for Jmol presentations

[Craig T. Martin]

--On Monday, September 13, 2004 12:06 PM -0400 Miguel [EMAIL PROTECTED] 
wrote:

Your file Support/JmolShell.js has some bad characters in it on lines 111
and 112. That prevents me from running.
Hmmm
The code around there is:
===
// Used by HelpHTML definition (only)
function GetTblRw(txt1,txt2)
{
return \tr align=\left\ valign=\top\\
+ \td\ + txt1 + \\/td\
+ \td\ + txt2 + \\/td\
+ \\/tr\;
}
// ===
// Figure out which browser is running
===
I can't figure out what is wrong. This runs on both Macs and PCs here...
How can I get information from the Java applet using JavaScript?
Specifically, I'd like to put up a window that parses Jmol replies from
user actions: id'ing atoms, getting distances, etc.?

The only mechanism that currently exists is to parse the output from the
MessageCallback handler. It is not pretty, but it is generally
Chime-compatible.
I can't find documentation for accessing MessageCallback from Javascript...
Craig Martin
Chemistry, LGRT 701   545-3299
http://www.chem.umass.edu/~cmartin 

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