[Jmol-users] Can anybody reproduce this issue for me...

[Jonathan Gutow]

I'm using Jmol 14.6.4 downloaded today.

1) Open a multiframe file (e.g. Spartan, Gamess, nwchem or something 
else). Navigate to the last frame. Open the console. Issue the command 
"getproperty moleculeinfo". In these multiframe files I get the wrong 
number of hydrogens in the molecular formula.

2) For any file (even a molecule pulled by name from servers using the 
"get MOL" menu item),  if you issue the above command multiple times the 
.nelements item changes value. The first time it seems to be correct, 
but after that it increases.

Can anybody else verify these?

Thanks,
Jonathan
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800 Algoma Boulevard FAX:920-424-2042
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Re: [Jmol-users] Jmol-users Digest, Vol 123, Issue 4

[Jonathan Gutow]

Bob,

Do you mean in the Jmol development files or a more generic system?

The benchmark database at NIST has computational results for some 
molecules using: http://cccbdb.nist.gov/

Or are you interested in the database of basis sets: 
https://bse.pnl.gov/bse/portal

Or something else?

Jonathan

On 8/24/16 4:13 AM, jmol-users-requ...@lists.sourceforge.net wrote:
> Date: Tue, 23 Aug 2016 06:27:43 -0500
> From: Robert Hanson 
> Subject: [Jmol-users] database of Gaussian or other
> To: "jmol-users@lists.sourceforge.net"
>   
> Message-ID:
>   

Re: [Jmol-users] page-developer request - Jmol Unplugged

[Jonathan Gutow]

Bob,

This is a great idea! 

Note: the Jmol WebExport feature automatically generates pages in the proper 
form to work.  On issue is that every single page generated for local use has a 
j2s directory.  That would be very inefficient for space.  Maybe we need to try 
to make that more efficient.

I would like to help, but I think I am too busy this summer.  I am running two 
major projects this summer (testing candidate anti-rhinovirus compounds for 
inhibition of rhinovirus infections and quantum computations on ionization 
potentials).  At present, I am barely keeping up with that.

Jonathan
Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-OshkoshOffice:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow/

> On Jun 28, 2016, at 5:57 PM, jmol-users-requ...@lists.sourceforge.net wrote:
> 
> Message: 2
> Date: Tue, 28 Jun 2016 09:00:57 -0400
> From: Robert Hanson 
> Subject: [Jmol-users] page-developer request - Jmol Unplugged
> To: "jmol-users@lists.sourceforge.net"
>   
> Message-ID:
>   
> Content-Type: text/plain; charset="utf-8"
> 
> Jmol page developers,
> 
> Today I am giving a workshop on the use of Jmol in general and inorganic
> chemistry. Tomorrow the subject is organic chemistry, and Thursday it is
> physical chemistry. These workshops are at the Universidad Mayor San Sim?n,
> in Cochabama, Bolivia. Please feel free to come and help me out!
> 
> While there is widespread fast internet in Bolivia, there are certainly
> times and places where it is not available. (One of those places is an
> auditorium where I am giving another presentation tomorrow.)
> 
> I have an idea that will change the way Jmol is used in many parts of the
> world. It will open up opportunities for millions of students and thousands
> of professors and high-school teachers to use Jmol. It's simple. I'm not
> sure exactly what to call it, but for now I am calling it "Jmol Unplugged".
> Here is the idea:
> 
> Somewhere - possibly SourceForge - we create a site where people can upload
> fully contained web site "packages" that amount to stand-alone web
> applications. For example, I just created this directory:
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites
> 
> where we find
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites/coolMolecules.zip
> http://chemapps.stolaf.edu/jmol/unplugged/sites/orbitals.zip
> 
> These are the fully-contained fully operational JavaScript versions of
> 
> http://www.stolaf.edu/depts/chemistry/mo/struc
> http://chemapps.stolaf.edu/jmol/orbitals
> 
> They can be downloaded to a laptop and -- provided the browser is set up
> for local file reading -- they will run totally disconnected from the web.
> 
> The conditions for curation would be something like this:
> 
> 1)  *For the most part* the site must work without an internet connection.
> It would be fine if it still has a few links to external pages that are not
> critical to the function of the site. But the primary function of the site
> would have to be self-contained. That means no use of NCI Resolver,
> PubChem, or RCSB, for example.
> 
> 2) The site is JavaScript only. Or, at least it is either Java-only or
> JS-only, and if it is Java only, that is clearly indicated in its file
> name.
> 
> 3) The contributor understands that they are giving away their site.
> Someone can now take it, change it, put it up somewhere on their own.
> Whatever. Maybe there's a licensing agreement that has to be worked out. I
> don't know.
> 
> Obviously we would  need some sort of introductory page with descriptions
> of the site packages. I think that would be a Wiki -- maybe even Wikipedia?
> Not sure about that.
> 
> We would have to think about whether we want to have these totally
> self-contained, with the  j2s directory, or not. My inclination is that we
> DO have them contain the j2s directory so that no changes to Jmol affect
> the site. But there might be other options there. I don't want to make this
> more complicated than it has to be.
> 
> I think there's a publication in this for anyone who wants to help organize
> it and get it off the ground. It will take some effort to standardize it,
> figure it out, and curate it.
> 
> Right now I am asking for anyone who wants to contribute their work to send
> me a link to a zip file that, when opened, contains your site and fits
> these criteria.
> 
> If you would let me use your site in my workshops and put them up
> temporarily at chemapps.stolaf.edu, send me a link today.
> 
> Thank you!
> 
> Bob
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> 
> If 

[Jmol-users] Thanks, switching to jsmol.min.nojq.js solved popup collisions with jquery dialogs...

[Jonathan Gutow]

Thanks to all on the list who pointed out that I was using the wrong
jsmoljs file since I am working in a system that uses jquery and
jquery-ui elements extensively.  Switching solved the collision problems.

Jonathan
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Re: [Jmol-users] Important Java changes - January 2014

[Jonathan Gutow]

Ouch!

I've been out of the loop for a while trying to get caught up on local work 
issues.  This does not sound good.  As I read the description from Oracle the 
only way to use Java in browsers that does not require a commercial certificate 
and a codebase compiled for each server (possibly you don't have to specify 
your codebase location in the jar, but I think you do) is to have each local 
user/intranet whitelist the particular jar from a particular source.  This may 
be OK within a large company infrastructure, but is not going to work for 
general users.

Have I misread this?

The most amusing thing about this is that the alternative (javascript and 
things like opengl) are no more secure for the same capabilities and so far 
much slower.

We still need the java application, but I guess we pretty much need to get 
everything converted to JSmol for web stuff.

Jonathan
On Nov 2, 2013, at 1:11 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Assuming the $500 certificate ensures that the signed Jmol java applet
 will not be blocked (?), I suspect there are a number of organizations that
 would be prepared to become sponsors...
 
 
 Quoting Robert Hanson hans...@stolaf.edu:
 
 I direct the discussion to
 
 https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias
 
 I believe this is the end of the unsigned Jmol Java applet along with
 JSpecView and JME.
 
 In addition, I'm pretty sure our free-be signing will not pass muster as a
 trusted authority:
 
 RIAs must contain two things:
 
   1. Code signatures from a trusted authority. All code for Applets and
   Web Start applications must be signed, regardless of its Permissions
   attributes.
   2. Manifest Attributes
   1. Permissions ? Introduced in 7u25, and required as of 7u51. Indicates
  if the RIA should run within the sandbox or require full-permissions.
  2. Codebase ? Introduced in 7u25 and optional/encouraged as of 7u51.
  Points to the known location of the hosted code (e.g.
  intranet.example.com) http://intranet.example.com.
 
 The latest upload of Jmol takes care of (2a). However, unless (2b) allows
 
 Codebase: *
 
 that's pretty much it for the signed applet as well. [Or maybe someone goes
 into the business of making custom signed Jmol applets for people!]
 
 Suggestions? Comments?
 
 If deployment of the signed Jmol applet is of interest, we will need a
 sponsor, because a certificate costs US$500/year. Let me know if you are
 interested in being that sponsor.
 
 At least we have a two-month lead on this (and I am headed for a visit with
 RCSB on Sunday).
 
 
 Bob

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] Problem with Jmol export to web?

[Jonathan Gutow]

We really should fix this.  My hope is to find some time to update export to 
web to generate pages that can us JSmol as well before next Spring.  
Unfortunately, my time is booked pretty solid, so I cannot make promises to do 
this.  Maybe we should make this patch to the templates as a temporary fix.

Jonathan
On Sep 16, 2013, at 6:57 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 1
 Date: Mon, 16 Sep 2013 18:45:58 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Problem with Jmol export to web?
 To: jmol-users@lists.sourceforge.net
   jmol-users@lists.sourceforge.net
 Message-ID:
   caf_yuvuge3yrk8oh6o9cdnfz0wyihno-qo9x4pbu0z5yeug...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 I think it works, but we have the added security features now that the
 unsigned applet can't access local files. So you have to go into the HTML
 and change this bit:
 
 if (jmoljarpath ==.){
 jmoljarfile=JmolApplet.jar; //use the unitary applet instead of
 incremental
 }
 
 
 to
 
 if (jmoljarpath ==.){
 jmoljarfile=JmolAppletSigned.jar; //use the unitary applet
 instead of incremental
 }
 
 I realize that that is not obvious.
 
 Bob

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] Jmol-users Digest, Vol 73, Issue 21

[Jonathan Gutow]

I guess I don't understand why the _ is necessary.  Although, I'm fine with 
whatever you want.  I have a tendency to use the underscore only when I think 
multiple words in camel case would be misunderstood.

Jonathan
On Jun 14, 2012, at 7:25 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 'd still like to add _ in the others so that one can do this:
 
 copy Jmol_*.js ...
 
 and they will all be together in my directories.

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] Jmol for iPads?

[Jonathan Gutow]

Uh..Oh...Now I'm embarrassed...this was workingI apologize to anybody who 
tried this.  The server side generation of images seems to be broken again.  I 
hope to have time to chase this over the weekend.  However, this means one more 
problem has been found and can be rectified. I will post again, when there is 
something working for people to try...

Jonathan
On Mar 29, 2012, at 4:39 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Presently, I'm working on this for the python scripted server that supports 
 the Web interface for the SageMath Package (www.sagemath.org).  
 
 If you want to see a server running this experimental technology, visit my 
 test server at  
 http://141.233.196.149:
 Login as: testJmol with a password of: test.
 This is a very wimpy old computer I keep running for test purposes.  Don't 
 expect very fast responses.  Anyway, if you click on any of the 
 pages/worksheets listed after you log in, you should see pages that use Jmol 
 to display 3-D objects.  The displays initially are static .png images 
 generated by JmolData.jar running on the server.  Jmol only becomes live when 
 you click on the make interactive button.
 
 So the way to do this is generate system calls from your scripting engine 
 like this:
 
 java -jar path to JmolData.jar -iox -s path to script that loads molecule 
 and sets view -J write 'filename.png'
 
 Jonathan

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-users] What's the status of Jmol and the IcedTea Plugin?

[Jonathan Gutow]

I found this thread in the archives

http://sourceforge.net/mailarchive/message.php?msg_id=28755656

This suggests that there is a workaround for getting Jmol to work with the 
IcedTea plugin.  I thought from reading it that IcedTea couldn't handle the 
segmented loading.  However, when I force the use of JmolApplet.jar instead of 
JmolApplet0.jar, I still have problems.  Did I miss something? Does it have to 
be the signed applet?

Thanks,
Jonathan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-users] Would the JSON NIO client mode improve the speed of server side image creation?

[Jonathan Gutow]

Can somebody who has experience using Jmol to generate image files on the 
server side comment on whether using the JSON NIO client mode would speed up 
response time?  If anybody has examples of how to do this I would appreciate 
it. 

I'm trying to help the SageMath people fix their 3-D rendering so that even 
devices that don't support JavaVMs will see something decent.   Presently, I'm 
working on the idea of launching Jmol with an OS call (from within Python code) 
along the lines of Jmol.jar -ionx -s scriptFileName -j write PNG PATHNAME.

Any help or suggestions would be welcome.

Thanks,
Jonathan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-users] Need some advice on server side static imageprocessing with Jmol...

[Jonathan Gutow]

Angel,

Thank you.  That wiki page looks like it describes exactly what I need.  As 
usual, I managed to overlook the wiki page with the documentation I needed.

Now all I have to do is find the time to write the Sage compatible python code 
to do this.

Jonathan
On Jan 21, 2012, at 8:32 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 From: Herr?ez S?nchez ?ngel angel.herr...@uah.es
 Subject: Re: [Jmol-users] Need some advice on server side static
   imageprocessing with Jmol...
 To: jmol-users@lists.sourceforge.net
 Message-ID: a57d6f5061c32e45801ceb118121c0377c2...@x-evs-01.uah.es
 Content-Type: text/plain; charset=iso-8859-1
 
 Hi Jonathan
 
 I've got no experience with servers, but
 
 http://wiki.jmol.org/index.php/Jmol_Application#Command_line_options
 
 To have the application exit once finished (e.g. after running a script), use 
 either of these: 
 Jmol.jar -x
 Jmol.jar --exit
 
 
 I think that -ionx is what Bob has always mentioned for automated tasks.
 
 
 Good luck!

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-users] Need some advice on server side static image processing with Jmol...

[Jonathan Gutow]

Dear Jmol Users:

I'm looking for somebody who has experience using Jmol on a server to generate 
.png images.  I am investigating whether this would be better for making static 
images in the SageMath package than Tachyon, which they presently use.

I've already tried passing some .jmol files of the kind the math software can 
generate to JmolData.jar, unfortunately they appear to contain some graphics 
entities that JmolData cannot handle.  Thus I believe I will have to run the 
full Jmol on the server to make this work.  My first question about this is,  
do we have a script command that will cause Jmol to quit?  It is important that 
the application exit when it is done with its job.  I can certainly add such a 
command, but have learned that we have so many things in Jmol that it is easy 
to overlook functionality that we already have.

Thanks,
Jonathan

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-users] Jmol.jar vs JmolData.jar

[Jonathan Gutow]

Ted,

Jmol.jar contains everything.  JmolData.jar is stripped down for use from the 
command line.  Bob Hanson or someone else who uses it can tell you more about 
it.  Primarily it is intended for server side and helper application uses.  
See: http://wiki.jmol.org/index.php/Files_Description#Notes

To get a .png out of Jmol.jar, you need to use script commands or the menus.  
See: http://chemapps.stolaf.edu/jmol/docs/#writeimage,frames for the 
description of the write command.  The script you use will depend specifically 
on the case you have.  However try something like:

write PNG filename

This should write the current frame to a .png file.

Jonathan
On Jan 21, 2012, at 7:22 PM, Ted Cohen wrote:

 In your recent post about automated processing, you refered to JmolData.jar
 but Angel wrote back referencing Jmol.jar.  I have googled for any information
 on Jmoldata.jar and did not find any.
 
 I have a need to create .png images from .pdb files.
 Could you send me the code that you use to get a .png
 from jmol and a bit of an explanation of what Jmoldata.jar is,
 how/if it relates to jmol.jar and where the documentation is for
 invoking it directly. I am assuming that typically, a user interacts
 with Jmol.jar (the pretty user interface) and JmolData.jar is called
 by the front end to do the heavy lifting?
 
 Thanks in advance,
 Ted
 

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-users] Issue with Jmol applet turning black

[Jonathan Gutow]

Ted,

This sounds like a memory problem.  Browsers seem to have different problems 
with the memory allocation to the Java applets.  What I have found is that 
killing and reloading the applet solves the problem.  With an applet size of 
400 x 400, about 5 simultaneously active Jmols is the safe limit.  My solution 
if you have more than one Jmol on a page is to put some to sleep to limit the 
total open to about 5.  For reloads I am not sure what the limit is, but I bet 
that if you reload the applet after every 5-10 loads the problem will go away 
in most browsers (no guarantee for IE, as I  have had trouble getting even 
standard buttons to work reliable in IE).

Jonathan
On Jan 17, 2012, at 7:58 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 4
 Date: Tue, 17 Jan 2012 14:58:40 -0600
 From: Ted Cohen j...@monona.us
 Subject: [Jmol-users] Issue with Jmol applet turning black
 To: jmol-us...@lists.sf.net
 Message-ID: 190c21bd7f64ff66ccdb07e4e35901cb.squir...@www.monona.us
 Content-Type: text/plain;charset=iso-8859-1
 
 jmol version is 12.2.10
 I am using the default, unsigned jar file
 I am serving it from a LAMP server that uses light speed.
 The client I am observing this on is Windows 7 Enterprise
 I am currently testing with both IE 9.0.8xxx and Firefox 9.01.
 I am using the Jmol.js interface with load inline.
 
 I have one applet in the web page.
 Based on user input, I change the
 structure file that is loaded.
 
 After an arbitrary number of inline
 loads, the applet turns black including the
 Jmol image in the lower right corner.
 
 I have seen it take as long as 36 structure loads
 to go black or as few as 2. Onve it turns black,
 it stays black. There are no warnings in red
 like a typical black screen would show. Everything
 in the java console looks normal.
 
 The applet is actually loading the new structure
 file as evidenced by the java console and also
 by  clicking the lower right of the applet
 (where the Jmol image should be). The menu
 displays, clicking on about... and then string
 shows that the correct structure is in fact loaded.
 
 About-system shows that only 5mb out of 495mb of
 ram avaialable to java has been used.
 
 I am going to run an experiment where I tear
 down (java console terminology) and recreate the
 applet to see if that changes anything.
 
 1) Has anyone seen this before?
 2) Is anyone else successfully doing repeated inline loads of
 a single applet?
 
 All suggestions appreciated,
 Thanks,
 Ted

 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] isosurface mep and mo on a plane

[Jonathan Gutow]

Xavier,
is it the typo in the first line?  You have plae instead of plane.  I have 
no experience trying to map MEP onto a plane, so am not sure if it would work 
otherwise.

Jonathan
On Nov 24, 2011, at 10:18 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 isosurface color absolute -0.1 0.1 plae xz mep
 but nothing gets displayed and the console says:
 isosurface created with cutoff=NaN min=0.0 max=0.0; isosurface count:0
 
 However, if I want to represent a MO on a plane using a very similar syntax
 it works just fine.
 isosurface color absolute -0.1 0.1 plane xz mo 10
 
 Am I missing any keyword?
 I have a test page showing my problem
 http://chemed.umr.umn.edu/~xavier/modelstest/
 
 Thanks
 
 Xavier

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] MO HOMO problem with GAMESS output

[Jonathan Gutow]

Jorg,

I'm pretty sure the problem is that we haven't included reading occupation 
numbers into the GAMESS reader yet.  I keep meaning to work on that, but it 
hasn't been a high priority.  GAMESS doesn't specify occupation numbers, just 
the total number of electrons in most of its calculations, so we will have to 
do a little counting...  I always do that manually and want my students to 
think about it, which is part of why I haven't pushed to get it done.

Jonathan
On Nov 15, 2011, at 9:03 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 From: J?rg Sa?mannshausen j.sassmannshau...@ucl.ac.uk
 Subject: [Jmol-users] MO HOMO problem with GAMESS output
 To: jmol-users@lists.sourceforge.net
 Message-ID: 20151019.15973.j.sassmannshau...@ucl.ac.uk
 Content-Type: text/plain;  charset=iso-8859-15
 
 Dear all,
 
 I am having a problem with a GAMESS output when I want to draw the HOMO/LUMO 
 orbitals. I stumbled over it by chance when I was looking into the HOMO/LUMO 
 of a large molecule and the problem can be repeated with a smaller molecule 
 like water. 
 I have attached the URL of the logfile from the GAMESS calculation
 http://sassy-design.de/tmp/water-SP.log.gz as well as the pictures 
 of the HOMO, generated that way:
 frame 1.1; isosurface cutoff 0.05 mo homo fill translucent 0.5
 http://sassy-design.de/tmp/homo.png
 and mo 5, generated that way:
 frame 1.1; isosurface cutoff 0.05 mo 5 fill translucent 0.5
 http://sassy-design.de/tmp/mo5.png
 
 As the list does not really like email attachments (for good reasons), in 
 brief: 
 MO5 should be the HOMO and when you draw it that way:
 frame 1.1; isosurface cutoff 0.05 mo 5 fill translucent 0.5
 you get the correct answer, i.e. that 'burger shaped' orbital with the two 
 lobes being the bread and the molecule being the meat. :-)
 (see above link)
 
 However, using that command here:
 frame 1.1; isosurface cutoff 0.05 mo homo fill translucent 0.5
 i.e. calling the HOMO directly, gives a different and wrong picture. It looks 
 more like higher, unoccupied orbital to me.
 (see above link)
 
 I am using jmol-12.0.49. I also tried the version Bob suggested in his email 
 from the  22 Jun 2011 with the same results.
 
 Anybody got any ideas? That seems to be a bug to me, at least with the GAMESS 
 output.
 
 All the best from a foggy London
 
 J?rg
 
 -- 
 *
 J?rg Sa?mannshausen
 University College London
 Department of Chemistry
 Gordon Street
 London
 WC1H 0AJ 
 
 email: j.sassmannshau...@ucl.ac.uk
 web: http://sassy.formativ.net
 
 Please avoid sending me Word or PowerPoint attachments.
 See http://www.gnu.org/philosophy/no-word-attachments.html

 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Something I think we should support...

[Jonathan Gutow]

Dear Jmol Users:

I just encountered the Science Code Manifesto, which essentially states that 
all computer code used for scientific analysis and modeling should be available 
for review.  Jmol already satisfies this, but I think it should be generally 
true.  It appears to have started with the Climate Code Foundation.  I 
encourage you to visit the web site and consider endorsing the Manifesto.


http://sciencecodemanifesto.org/

Jonathan
 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Something I think we should support...

[Jonathan Gutow]

Actually, I think programs like Gaussian, which don't allow us to look at the 
code, so we cannot judge if they are actually doing what they say, are somewhat 
problematic.  They at least try to document the math they are doing, but as you 
know without seeing how they actually implement the calculations,  you cannot 
be sure they've done what they say.

Other examples that are in this problematic area are Mathematica, Maple and 
the data analysis packages Origin, Sigma Plot and IGOR.  IGOR at least 
references papers and texts on every algorithm they implement, but you still 
cannot look at the code and check.

The longer I have worked with information that is either produced or 
manipulated by computer programs, the more convinced I've become that the code 
should be viewable by anyone who has to use that information or judge its 
quality.

My, rather opinionated;), 2 pennies.

Jonathan
On Oct 14, 2011, at 2:43 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Date: Fri, 14 Oct 2011 10:42:41 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Something I think we should support...
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   caf_yuvxnxfoadocxgfnremqdzfyvgryotku80epxyu6nsxs...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Thanks, Jonathan. I just sent in my endorsement. I think the wording is not
 perfect. What exactly is processing data for example? But I guess you
 could say that programs such as Gaussian would be excluded because they are
 the ORIGINATORS of the data, not specifically for processing the data. I
 don't know.
 
 Bob
 
 On Fri, Oct 14, 2011 at 8:10 AM, Jonathan Gutow gu...@uwosh.edu wrote:
 
 Dear Jmol Users:
 
 I just encountered the Science Code Manifesto, which essentially states
 that all computer code used for scientific analysis and modeling should be
 available for review.  Jmol already satisfies this, but I think it should be
 generally true.  It appears to have started with the Climate Code
 Foundation.  I encourage you to visit the web site and consider endorsing
 the Manifesto.
 
 
 http://sciencecodemanifesto.org/
 
 Jonathan

 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] image snapshot

[Jonathan Gutow]

I developed some code for switching to the signed applet on-the-fly for the 
SageMath package.  Then the user only gets warnings if they try to do something 
that requires writing to their disk.  This required a small change to the 
standard Jmol.js libraries, but if people think this would be a useful option 
we could add it to Jmol.js

I'm thinking of something along the lines of: jmolSwitchtoSigned(appletId, 
scriptforSignedApplet), which would destroy the unsigned applet load a signed 
applet and run the script.  It would be up to the page designer to make sure 
that the signed applet was passed information in the script to recreate the 
state of the unsigned applet.

Jonathan
On Sep 2, 2011, at 12:22 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 From: Paul Pillot paul.pil...@ac-orleans-tours.fr
 Subject: Re: [Jmol-users] image snapshot
 To: jmol-users@lists.sourceforge.net
 Message-ID: 851740da-5d00-45c4-bcb4-a8cc15d6b...@ac-orleans-tours.fr
 Content-Type: text/plain; charset=iso-8859-1
 
 If you have the signed applet then the Jmol sign at the bottom right corner 
 should be in red and should read Jmol_S
 Otherwise, if it's grey and reads Jmol then it's the unsigned applet.
 If you don't mind using the signed applet, it's the easiest solution. The 
 only thing is that the user will have to accept it, in order to use it.
 -Paul

 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Should translucency be additive?

[Jonathan Gutow]

Dean,

I'm trying to look at what you describe and don't think I understand what to 
look for.Are you saying that if you put  two 0.5 translucent planes in 
front of an opaque item the intensity of the opaque item is the same as when 
you put only one 0.5 translucent plane in front?  If that is what you are 
describing, that is not what I see (at least not with the development version, 
I'm working with).

Jonathan
On Aug 8, 2011, at 5:42 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 5
 Date: Sun, 7 Aug 2011 23:41:44 -0400
 From: Dean Johnston djohnsto...@gmail.com
 Subject: [Jmol-users] Should translucency be additive?
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   capbny6jh9uj1s+zkgvjeey2vgimqpn6k_dy5u5tmygh-44n...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Jmol'ers,
 
  I just noticed an interesting effect in Jmol.  I have a model with several
 planes having different levels of translucency.  But Jmol only seems to use
 the translucency of the frontmost plane when looking at something that falls
 behind two translucent planes.  I suspect this is in the name of efficiency,
 but didn't know if anyone else had noticed this.
 
 Dean

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] display/hide isosurfaces

[Jonathan Gutow]

You can use the command isosurface list to get the names created by default.  
They are usually of the form isosurface1, etc.  However, I recommend giving 
any surface you want to control a name when you create it.  The first word 
after the command isosurface will be used as the name.

Jonathan.

P.S. Note that a GUI surface tool, which will allow you to manipulate surfaces 
is in the works for the next release.  Probably will only have slicing 
(slabbing) surfaces in 12.2, but we'll see how far I get.  Until we know how 
heavy weight it is, I can't tell you whether we'll put it in the applet.


On Jul 27, 2011, at 6:16 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 From: Daniel Carbajo daniel.carb...@gmail.com
 Subject: Re: [Jmol-users] display/hide isosurfaces
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   CABw+tYc16BiT=1BdidpJN8V=xfnvz3aod4v_c90m-q3jatp...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 The problem is that I do not know which is the isosurface displayed... so I
 want to hide everything and show the isosurface that was displayed before
 hiding, I do not know the ID... I do not know if I am clear, but I think
 that at the end I will put a show/hide checkbox for the structure and a
 drop-down menu for the surface with the options hide, show solvent
 accessible surface, show solvent excluded surface, I think that way I
 avoid any problem, what do you think?
 Thanks again Robert.

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-users] Customized pop-up menu not always activated by right-click?

[Jonathan Gutow]

Dear Jmol Users:

I'm trying to track down an odd issue I and some others are seeing on web  
pages that use a custom pop-up menu within Jmol.  What I would really like is 
for people to try this web page with different OS/Browser combinations and 
report to me if they see the issue.  What we're seeing is that the pop-up only 
works if you right-click in the bottom or right third of the Jmol applet.  So 
far we've verified it with the following:

OSX 10.6.8
Firefix 5
Chrome 12.0.742.112
java version 1.6.0_26
Java(TM) SE Runtime Environment (build 1.6.0_26-b03-384-10M3425)
Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02-384, mixed mode)

and the 32 bit  mode as well.

Please try this web page: 
http://www.uwosh.edu/faculty_staff/gutow/right-click_test/right-click_test.html

I've also verified that the problem does not occur with FF or Chrome under 
Ubuntu Linux.  I mostly need Windows testers now.  I'm suspicious of the MacOS 
JVM.  If you've got a different VM installed on a MacOS system, I'd really 
appreciate you giving this a try and reporting back.

Thanks,
Jonathan

 
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] Customized pop-up menu not always activated by right-click?

[Jonathan Gutow]

Jason,

The below does help.  I can locally reproduce the effect with a 700 x 700 Jmol 
and the default menu.  Thus it looks like a problem related to the size of the 
menu relative to the applet frame... 

Now can we isolate it to just the Mac JVM or does this show up with other 
OS/JVMs?

Jonathan
On Jul 5, 2011, at 2:58 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Here's a test that might help track things down: make a jmol applet big 
 enough so that the default (long) menu fits inside of it with room to 
 spare.  Then we can see if it is a custom menu issue or an issue with 
 all menus.  This is difficult to test now because the size of the 
 demonstrations are all smaller than the height of the default menu, so 
 no matter where I right-click, the menu always extends below the border 
 of the java frame.

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-users] Customized pop-up menu not always activated by right-click?

[Jonathan Gutow]

Another piece of the puzzle (thanks Nick!).  Most of the time this works OK in 
Safari on MacOS X.  Note that when I was doing my original build of the test 
page, I got it to act funny in Safari as well, but now when I go back it seems 
to work OK.  I definitely still see the dead area in Chrome and FF on MacOS X.

Anybody tested those on Windows?

Jonathan

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-users] Customized pop-up menu not always activated by right-click?

[Jonathan Gutow]

Angel,

Thank you.  I think that pins down the problem combinations:

MacOS X
Chrome
FF
Java 1.6.0_26 in 32 and 64 bit modes.

Usually works on Safari and MacOSX.

I'll see if I can test on older Mac JVMs.  Although, I am less suspicious of 
the JVM now since Safari seems to work.  FF and Chrome may be messing up the 
click locations that are passed to the applet.

The specific symptom is that the right-click only works if the menu is wide 
enough or tall enough to reach the right edge or bottom of the applet when it 
opens.

As the menu is still usable, I may give up after testing older JVMs.  This is 
beginning to sound more like a bug report for Chrome or FF.

Jonathan
On Jul 5, 2011, at 3:38 PM, Angel Herráez wrote:

 Hi Jonathan
 
 In summary it works fine for me under WinXP, Sun/Oracle's Java 1.6.0_25 with 
 all of these:
 Firefox 5.0
 MSIE 8
 Chrome 14.0.803.0 dev-m
 Safari 5.0.5 (7533.21.1)
 
 
 The custom menu opens at any position. Initially I occasionally got instead 
 the default 
 browser popup menu, but that was because it is not clear where are the limits 
 of the 
 JmolApplet, so I sometines clicked in the surrounding area. Once I change the 
 background 
 color the issue does not appear.
 
 
 
 
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 Why? It contains a definitive record of application performance, security 
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800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-users] File reader not found :Pdb

[Jonathan Gutow]

Unfortunately, you are probably running  up against the default JVM 
installation on Ubuntu.  They recently decided that the completely free 
IceTea stuff was now up-to-snuff.  If you take your test Ubuntu system and 
install the Sun Java it should work.  I do my development on Ubuntu and 
everything works fine with the Sun Java.  I think the people at Ubuntu jumped 
the gun slightly.  IceTea is almost complete, but not quite.

Browsers crashing is odd behavior.  I just saw some features of Jmol not load 
properly or behave strangely when using the non-Sun Java.  Which browsers are 
you testing on Ubuntu?  I find Chromium and FF work fine.

Jonathan
On Jun 19, 2011, at 10:15 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 3
 Date: Sat, 18 Jun 2011 18:44:19 -0400
 From: J ZHANG jzha...@clemson.edu
 Subject: Re: [Jmol-users] File reader not found :Pdb
 To: jmol-users@lists.sourceforge.net
 Message-ID: 5322CB4339EC4CCDBD84DB547D4B4D4F@JemisonHP
 Content-Type: text/plain; charset=iso-8859-1
 
 I tested the application under several browser from different system only 
 browsers from Ubuntu does not work, So I don't think some files are missing.
 later, I found a solution for this problem : when use 
 jmolInitialize('./jmol12/',true); browsers from Ubuntu crashed, however 
 switch to jmolInitialize('./jmol12/'); solve the problem. 
 the only problem left now is some commands in jmol 12 do need signed Applet.
 
 
 From: Robert Hanson 
 Sent: Friday, June 17, 2011 11:59 PM
 To: jmol-users@lists.sourceforge.net 
 Subject: Re: [Jmol-users] File reader not found :Pdb
 
 
 You are missing some files. Just unload all the applet files into your 
 directory again.
 
 
 2011/6/17 J ZHANG jzha...@clemson.edu
 
  Hi, I am trying to deploy a jmol applet application on server, Browsers 
 (except IE 9 64-bit) on Windows 7, on Mac all pass the test ,and on linux 
 like centOS 5 also pass the test. but Ubuntu  does not work and gives out 
 message in the applet :
 
  File reader not found :Pdb
 
  I already enabled the applet in Browser(Jmol_S in the right bottom corner 
 of applet frame), sometime in the right bottom corner show the seconds[over 
 100s] of loading the Jmol applet.
 
  Anyone knows how to fix it ? or anyone have met this problem? 

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] Jmol, MacOS, FF Safari...

[Jonathan Gutow]

I am trying to work around this in SAGE by controlling the number of applets 
open at once.  There are two problems:

1) Safari (and probably FF) on MacOS don't appear to properly free up memory 
when an applet is destroyed.  Chrome on MacOS does, as I have no problems as 
long as I limit the number of applets open at once.
2) We don't have a good way of estimating how much memory the applets are using 
in javascript.  Could we get javascript access to the information in the 
system menu or have I just missed how to do that?  Now what I am doing is 
just counting applets.  This usually works, but is a problem if one of the 
applets is displaying a lot of surfaces.  Then it uses more than the average 
amount of memory.

Jonathan
On Mar 29, 2011, at 8:07 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Jmol, MacOS, FF  Safari...
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   AANLkTi=ZKcdEEXbgKAO2imTCtGd49etNCEWkV4=_h...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 That's right. It's not a plug-in. You can't launch a huge number of applets
 on a page. Can SAGE work around that?
 
 On Mon, Mar 28, 2011 at 8:08 AM, Jonathan Gutow gu...@uwosh.edu wrote:
 
 Dear all,
 
 I've been working this last week on Jmol in SAGE math (www.sagemath.org).
 I thought people might be interested in what I've learned.  In the process
 I've unearthed a number of issues on MacOS.
 
 a) When launching a lot of applets on a page in FF sometimes not all the
 applets finish initializing.  There appears to be a memory/process collision
 problem.  It is so intermittent that I have not been able to pin it down.
 Things seem to be worst on 64 bit installations.
 
 b) Safari also has problems with launching a lot of applets.  This one I
 could trace to memory issues.  I think Safari has a memory leak as the
 problem occurs even after most of the applets are forced to close.
 Interestingly, this problem shows up as a security violation when calls
 attempt to get an image from the applet as a string.
 
 c) Jmol works very well in Chrome on MacOS.  I was unable to produce any of
 the oddities I saw in FF or Safari.
 
 Notes:
 1) The tests involve launching pages that have lots of Jmols on them.  It
 is very easy to run up against the memory limits of the JVM in the browser,
 so the launches are carefully controlled to be sequential and no more than 4
 of the applets are allowed to stay open simultaneously.  A repeating
 javascript process replaces an already open Jmol with an image before
 opening the next one.
 2) To see examples of what the pages in Sagemath look like go to 
 http://http://141.233.197.45:/home/pub/0
 141.233.197.45:/home/pub/0
 3) FF and Chromium work very well on Ubuntu Linux
 4) I haven't performed these demanding tests on a Windows machine yet.
 
 Jonathan
Dr. Jonathan H. Gutow
 Chemistry Department gu...@uwosh.edu
 UW-Oshkosh   Office:920-424-1326
 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
 
 

 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Jmol, MacOS, FF Safari...

[Jonathan Gutow]

Dear all,

I've been working this last week on Jmol in SAGE math (www.sagemath.org).  I 
thought people might be interested in what I've learned.  In the process I've 
unearthed a number of issues on MacOS.

a) When launching a lot of applets on a page in FF sometimes not all the 
applets finish initializing.  There appears to be a memory/process collision 
problem.  It is so intermittent that I have not been able to pin it down.  
Things seem to be worst on 64 bit installations.

b) Safari also has problems with launching a lot of applets.  This one I could 
trace to memory issues.  I think Safari has a memory leak as the problem occurs 
even after most of the applets are forced to close.  Interestingly, this 
problem shows up as a security violation when calls attempt to get an image 
from the applet as a string.

c) Jmol works very well in Chrome on MacOS.  I was unable to produce any of the 
oddities I saw in FF or Safari.

Notes:
1) The tests involve launching pages that have lots of Jmols on them.  It is 
very easy to run up against the memory limits of the JVM in the browser, so the 
launches are carefully controlled to be sequential and no more than 4 of the 
applets are allowed to stay open simultaneously.  A repeating javascript 
process replaces an already open Jmol with an image before opening the next one.
2) To see examples of what the pages in Sagemath look like go to 
http://141.233.197.45:/home/pub/0
3) FF and Chromium work very well on Ubuntu Linux
4) I haven't performed these demanding tests on a Windows machine yet.

Jonathan
 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] I think the vibration animation state is being left out of the state...please check...

[Jonathan Gutow]

Dear All:

I think the vibration animation state is being left out of the Jmol generated 
state script for versions of Jmol 12.0.26 and above (may have started earlier). 
  Can others please verify that when they save a state script for a molecule 
that is showing an animation of the vibration and reload the state script the 
reloaded molecule is not animated?

Thanks,
Jonathan
 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Does anybody remember if the cut-off syntax for isosurface changed between 11.8 and 12.0?

[Jonathan Gutow]

I am in the midst of processing internal grant proposals so haven't  
got time to dig. Does anybody remember if the cut-off syntax for  
isosurface changed between 11.8 and 12.0?  The reason I ask is that  
some of my old web pages that use the isosurface command to display  
surfaces from .cube files generate a syntax error related to the cut- 
off in version 12.0 but not 11.8.

Thanks,
Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] molecular orbital linear combinations

[Jonathan Gutow]

Cool!  I wish I had time right now to play with this a little.  In a  
couple of weeks I start talking about MOs in p-chem.   I'll see if I  
can find a use for this.

Jonathan
On Feb 9, 2011, at 11:36 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Wed, 9 Feb 2011 08:39:01 -0600
 From: Robert Hanson hans...@stolaf.edu
 Subject: [Jmol-users] molecular orbital linear combinations
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   AANLkTinnbf7TaBc9CG-sFo6DLGVHv=1kp0ewhfs3f...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 I had a little time in the airport Monday and thought I would spend it
 constructively.

 If you are interested in being able to visualize linear combinations  
 of
 molecular orbitals, take a look at

 http://chemapps.stolaf.edu/jmol/docs/examples-12/motest/

 This simple page scans a file for MOs, jumping to the frame that  
 contains
 them, and creates two drop-down lists listing all the orbitals.

 Moving the slider (and releasing the mouse) should display a linear
 combination of the two selected MOs. It uses the signed applet, so  
 you can
 load any file you want.

 The new command syntax is:

 MO [c1 n1, c2 n2, c3 n3,]

 For example:

 MO [0.5 20, 0.5 21]

 The coefficients are automatically normalized, so

 MO [1 20 1 21]

 is the same as

 MO [0.5 20 0.5 21]

 I'd be interested in knowing if any of the orbital viewing programs  
 out
 there allow such combination.

 Bob

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Jmol.app default dir in OS X?

[Jonathan Gutow]

Eric,

I'm not sure how to do everything you want.  But some things you  
should look at:

1) I use automator to build a double clickable application that can be  
put in the doc to launch Jmol.  You have to make it for the directory  
you have your Jmol.jar located in.

2) I am not aware of a way to pass the path to use to Jmol on launch  
except as a script.  Bob? Angel? Nico?  So one solution might be to  
have a script file in the directory with the set defaultdirectory  
directive in it.  Then open that script in Jmol.  I'm not sure if that  
is much of an improvement, but it s an idea.

3) Copy and paste I can help you with.  In finder use the normal cmd-C  
to copy.  When you switch to Jmol you have to use the *nix/Windows  
convention of cntl-V to paste not cmd-V.  At least it works on my  
computers.  It may be easier to get the proper path copied from a  
terminal window.

Hope this helps,
Jonathan
On Jan 17, 2011, at 10:10 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Subject: Re: [Jmol-users] Jmol.app default dir in OS X?
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   AANLkTi=cc-mrraffw0xy4tddypypvopnnm8pbspjg...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 On Sat, Jan 15, 2011 at 4:57 PM, Eric Martz  
 ema...@microbio.umass.eduwrote:

 Could someone please explain to me how, in OS X (I am using leopard),
 to most easily set the Jmol.app default directory? The only ways I
 have found are so cumbersome that I have ended up littering my
 directory tree with many copies of (different versions of) Jmol.app.
 I double click on Jmol.app in the directory that has the relevant
 scripts and PDB files.

 Ideally, I would like a button in Finder that would start Jmol.app,
 setting the current directory to the one current in Finder. Open
 Terminal Here is an application/droplet/script that does this for
 Terminal -- not sure if it could be modified to open Jmol.app.

 Second best would be a way to drag and drop, or copy and paste, a
 directory path that I have located in Finder. If I could easily copy
 that path to the clipboard, then I could paste it into the Jmol
 Script Console after typing cd . I don't know how to copy a path
 from Finder to the clipboard.

 Obviously, I don't want to have to hand-type the filepath into a Jmol
 cd command.

 Thanks! -Eric


  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Language about Jmol Web Page Maker

[Jonathan Gutow]

Li,

Hello, and thank you for the report.  We could definitely use help on  
the translation.  As far as I know we only have a spanish translation  
of the help/instructions for web-export.  Basically you will need to  
duplicate the the files with .html extensions in the following  
directory of the Jmol source tree and translate them.

http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/openscience/jmol/app/webexport/html/

Make sure the translated files have the proper language extension  
added to them: eg. Installing_Applet_XX.html, where the XX is the two  
letter language code.  Then zip all the files up and send them to me.   
I, with Angel's help, will get them inserted.  (Angel is there a  
better way?)

Can you send me copies of the generated page with the widget problem  
and a copy of one you corrected (or send me links)?

Thanks,
Jonathan
On Dec 16, 2010, at 7:24 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 6
 Date: Fri, 17 Dec 2010 09:24:20 +0800
 From: Anbang Li lianb...@gmail.com
 Subject: [Jmol-users] Language about Jmol Web Page Maker
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktikinktzgwx+3f09cc8j9austffdr7yh2ridx...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Hi, all,

 When I click the button of Export one or more views to a web page on
 the toolbar of Jmol Application, the Jmol Web Page Maker dialog
 appears. I have something to talk about it.

 First of all, no matter what language I choosed, the text below the
 label of Introduction is always in English. I want to ask, how can I
 translate them?

 Second, when I view the created webpage, I found the encoding of the
 normal text in the webpage is right, but the encoding of the widgets
 is NOT right, I have to change the encoding of the widgets ( GB2312
 for zh_cn) by hand. Maybe this need to be checked.

 Best wishes,
 LI An-Bang

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Solved my own problem

[Jonathan Gutow]

Jeff,

I'm confused.  What you deleted should be invisible text that is there  
for record keeping, so we can trace errors in creating the page.  It  
appears that the example you provided was created without the files  
being where they were expected to be.  I apologize if you've already  
explained how the pages were created.  I seem to have missed the  
beginning of this discussion.

If the text you deleted is accurate, I don't think the pages created  
by export to web should be working.  Did you have to go back and put  
lots of files in the directory created by Jmol?

I'm pretty swamped until this weekend, but if things don't get better  
zip up and example directory created by export to web and send it to  
me.  I'll try to look at it as soon as possible.

Jonathan
On Oct 5, 2010, at 1:35 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 4
 Date: Tue, 5 Oct 2010 14:34:57 -0400
 From: Jeff Hansen jhan...@depauw.edu
 Subject: Re: [Jmol-users] Solved my own problem
 To: jmol-users@lists.sourceforge.net
 Message-ID: 79b07a49-e80e-482c-89d2-da5ec28fe...@depauw.edu
 Content-Type: text/plain; charset=iso-8859-1

 The problem does not occur when the students are working in their  
 own local folders.  What I showed you was all that I deleted - just  
 text within a pre /pre tag.

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Can't visualize molecular orbitals from GAMESS(US) output

[Jonathan Gutow]

Marco,
The optimized results should be in the last frame.

Jonathan
On Oct 4, 2010, at 1:30 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 4
 Date: Mon, 4 Oct 2010 13:49:46 -0400
 From: Marco Zimmer-De Iuliis marcoz...@gmail.com
 Subject: Re: [Jmol-users] Can't visualize molecular orbitals from
   GAMESS(US)  output
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktik=woqi97dyhzgfhhd8ovjvcjq5oukow+tdf...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Thanks for your help.

 That worked - the molecular orbitals is no longer greyed out and I  
 can
 display them, but the geometry of the molecule is not optimized - it  
 is
 showing the second step of the optimization process with molecular  
 orbitals
 displayed on those coordinates.

 Shouldn't the molecular orbtials be displayed on the optimized  
 structure?

 Thanks again,
 Marco

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] error with jmolColorPickerBox

[Jonathan Gutow]

Angel,

I think Piero and I straightened this out.  Piero, correct me if I'm 
wrong...:).  Angel is correct that the second array must be a JavaScript array, 
not a string.

Angel,

Just so you know, I did modify JmolColorPicker.js to accept the same kind of 
array structure as most Jmol.js command in place of a script.   This was 
specifically for Piero's application.   See the advanced usage section of the 
documentation in the current version (1.2).

Jonathan
On Aug 15, 2010, at 3:31 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 1
 Date: Sat, 14 Aug 2010 11:23:25 +0200
 From: Angel Herr?ez angel.herr...@uah.es
 Subject: Re: [Jmol-users] error with jmolColorPickerBox
 To: jmol-users@lists.sourceforge.net
 Message-ID: 4c66608d.23204.5593...@angel.herraez.uah.es
 Content-Type: text/plain; charset=us-ascii
 
 Piero, I think your problem may have originated in some mismatch that existed 
 between 
 instructions and the actual functions in JmolColorPicker.js.
 
 
 var colorScript = [setAtomColor, 'atomColor'];
 
 I'm not sure why you have that. it should be a string with a Jmol script, not 
 an array.
 
 
 jmolColorPickerBox(colorScript, '[100,100,100]');
 
 Here you need to remove the quotes. The 2nd parameter must be a javascript 
 array:
 jmolColorPickerBox(colorScript, [100,100,100]);
 
 (this is the piece that was wrong in the doc)
 
 If that fails, get the updated version from
 http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/openscience/jmol/app/webexp
 ort/html/JmolColorPicker.js

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] Use gamess.log file to make a Jmol applet

[Jonathan Gutow]

Marco,

I use GAMESS to generate many of my web pages.  You can look at  
examples at my web site.  See the Jmol stuff and the chemistry  
tutorials.

Note: Angel is correct.  You should start by opening the files in the  
application (Jmol.jar) and set up the view you want.  Then use the  
Export to web option to generate a skeleton web page that you can add  
text to in a WYSIWYG editor.  A tutorial on this is also available on  
my web site (includes an intro on controlling what things look like in  
Jmol as well):

http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/Export_to_web_tutorial.shtml

You might also consider buying Angel's book, which explains a lot.

Jonathan
On Jul 31, 2010, at 1:23 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Fri, 30 Jul 2010 11:41:48 -0400
 From: Marco Zimmer-De Iuliis marcoz...@gmail.com
 Subject: [Jmol-users] Use gamess.log file to make a Jmol applet
 To: jmol list serve jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktin8eherre4ybb4bwk4nfw20b_an+xw6xhasf...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Hello all,

 I am very new to Jmol, and this may be a very basic question, but I  
 would
 like to create jmol applets of molecules that I have optimized and  
 performed
 vibrational analyses on using GAMESS.

 I use the GAMESS-US package and usually the optimization steps and
 vibrational data are both in the .log file from GAMESS.

 I have Jmol and I can open the log files and see my molecules, but I  
 am
 unsure how to go about making an applet I can use.  I would like to  
 be able
 to put it on a web page as aswell as in a power point presentation.

 Is there any tutorials out there for newbies that someone can  
 recommend?

 My thanks in advance.

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] New version of jmolColorPickerBox that may solve Piero's problem

[Jonathan Gutow]

Piero,

As Angel pointed out there was a typo in the instructions on the web  
page (Still in the .js file, I will fix that later today:).  In  
addition you are misunderstanding the format for the array.  See below  
for corrections...

Jonathan
On Jul 20, 2010, at 6:32 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Tue, 20 Jul 2010 12:22:52 +0100
 From: P.Canepa pc...@kent.ac.uk
 Subject: Re: [Jmol-users] New version of jmolColorPickerBox that  may
   solve   Piero's problem
 To: jmol-users@lists.sourceforge.net
   jmol-users@lists.sourceforge.net
 Message-ID:
   42054e10c02cd44d81ef510077a30a073829ed4...@mapi.ad.kent.ac.uk
 Content-Type: text/plain; charset=us-ascii

 I got your script

 I was trying to use it

 my HTML page has  the script set like that


 script type='text/javascript'
var Colorscript = new Array (setAtomColor);
try var Colorscript = [setAtomColor, atomColor];

jmolColorPickerBox(Colorscript, 'rgb(100,100,100)');
why the double quote at the end of the line? Note the change to [ from  
( below.
try jmolColorPickerBox(Colorscript, 'rgb[100,100,100]');
 /script

 The array Colorscript should be the array  which include the name of  
 the function to call

 the function setAtomColor() is  written as :

 var atomColor = ;
  function elementSelected(element){

   setValue(select none; halo off; label off);
   setValue(select   + element + ; halo on; label on);

   atomColor = ' color  + element;   
   return atomColor;
  }



 function setAtomColor (rgbCodeStr, Colorscript , jmolApplet0,  
 atomColor){
try function setAtomColor(rgbCodeStr, Colorscript,appletID){
   var finalColor =+ atomColor +   + rgbCodeStr +  ;
   return finalColor;
instead of returning the script send it to Jmol.
eg.
jmolScript(finalcolor,appletID);
 }

 I think I got your explanation wrong  in the headings of your  
 script. Is the rgbCodeStr the color selected by jmolColorPickerBox ?
 Thanks a lot, Piero

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] New version of jmolColorPickerBox that may solve Piero's problem

[Jonathan Gutow]

Thanks hadn't caught that.  Will fix.

Jonathan
On Jul 19, 2010, at 1:36 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Subject: Re: [Jmol-users] New version of jmolColorPickerBox that may
   solve   Piero's problem
 To: jmol-users@lists.sourceforge.net
 Message-ID: 4c448b67.11233.37dd2...@angel.herraez.uah.es
 Content-Type: text/plain; charset=US-ASCII
 
 Jonathan,
 
 there is an error in the instructions on that web page
 http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol%2
 0Color%20Picker%20Test.html
 it says
 
 Usage
 Where ever you want a popup color picker box include a script like
 script type=text/javascript
 var scriptStr2 = 'select carbon; color atom $COLOR$;';
 jmolColorPickerBox(scriptStr2, rgb(100,100,100), colorBox1, 0);
 /script
 
 
 But the correct syntax for the second argument is [100,100,100]

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-users] New version of jmolColorPickerBox that may solve Piero's problem

[Jonathan Gutow]

Piero (and anyone else interested):

Please try JmolColorPickerBox.js version 1.2.  I have added the option to pass 
an array of information that calls a function defined by the page programmer.  
The link is: 
http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol
 Color Picker Test.html

See towards the bottom for a link to the .js file and syntax information.  

Please let me know if this works.

Jonathan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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[Jmol-users] e: problem setting element colors with JmolColorPickerBox

[Jonathan Gutow]

Piero,

Already started on it.  I only get about 1 hour a day to work on this  
stuff.  I'll let you know when I finish it.  I hope by the end of the  
week.

Jonathan
On Jul 15, 2010, at 7:57 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Thu, 15 Jul 2010 13:21:52 +0100
 From: P.Canepa pc...@kent.ac.uk
 Subject: Re: [Jmol-users] problem setting element colors  with
   JmolColorPickerBox
 To: jmol-users@lists.sourceforge.net
   jmol-users@lists.sourceforge.net
 Message-ID:
   42054e10c02cd44d81ef510077a30a073829ed4...@mapi.ad.kent.ac.uk
 Content-Type: text/plain; charset=iso-8859-1

 Dear Jonathan,
 In the end will you make the extension? when you have something  
 ready I am willing to test it.
 Thanks , Piero

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] problem setting element colors with JmolColorPickerBox

[Jonathan Gutow]

Thanks Bob.  I'll look at that. 

Jonathan
On Jul 14, 2010, at 11:20 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 Date: Tue, 13 Jul 2010 17:16:15 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] problem setting element colors with
   JmolColorPickerBox
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktikdotvhprd1amwvidpns7ccivhkbvz_jtrru...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 That sounds like a great idea, Jonathan. You could follow the method I used
 for buttons:
 
 // bh 1/2010  -- adds option to run a JavaScript function from any Jmol
 control.
 //   This is accomplished by passing an array rather than a
 script:
 //   jmolHref([myfunc,my param 1, my param 2], testing)
 //   function myfunc(jmolControlObject, [myfunc,my param 1,
 my param 2], target){...}
 //   and allows much more flexibility with responding to
 controls
 
 Bob

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] problem setting element colors with JmolColorPickerBox

[Jonathan Gutow]

Actually it would not be hard to make an extended version of the ColorPickerBox 
that doesn't take a script but a name of a function which would generate the 
scriptstr with $COLOR$ in the appropriate place.  Is that what you need?

Jonathan
On Jul 13, 2010, at 12:54 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Piero,
 
 Please include the part where you call the ColorPickerBox.  You are supposed 
 to pass the ColorPickerBox the string, which in the formulation you provide 
 may not have the necessary space before the color. 
 
 I'm unclear on exactly what you are trying to do.  The ColorPickerBox 
 substitutes the color the user chooses for $COLOR$ in the script you provide. 
  Another possibility is that you are running up against the fact that 
 JmolColorPickerBox is writing html and javascript to your page dynamically, 
 but does not have a mechanism for updating the script once the box is 
 created.  If that is the problem I will have to think on it a little.  We can 
 also consider making a version that passes the color to a function of your 
 choosing.  Then you could send a script that is modified on the fly.
 
 Jonathan
 On Jul 13, 2010, at 8:03 AM, jmol-users-requ...@lists.sourceforge.net wrote:
 
 Date: Tue, 13 Jul 2010 11:44:57 +0100
 From: P.Canepa pc...@kent.ac.uk
 Subject: [Jmol-users] problem setting element colors with
  JmolColorPickerBox
 To: jmol-users@lists.sourceforge.net
  jmol-users@lists.sourceforge.net
 Message-ID:
  42054e10c02cd44d81ef510077a30a073829ed4...@mapi.ad.kent.ac.uk
 Content-Type: text/plain; charset=us-ascii
 
 Dear all, 
 
 do you know why  JmolColorPickerBox( doesn't work ? The string  scriptColor 
 = ' color  + element +  $COLOR$'; s correctly written. 
 
 
 
 var scriptColor =  ; 
 function elementSelected(element){
 
  scriptColor = ' color  + element +  $COLOR$';   
  return scriptColor;
 }

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] Coloring A molecular dynamically....

[Jonathan Gutow]

Jay,

With Angel's help I am in the process of finishing the debugging of  
the javascript for the colorpicker widget.  As Angel says presently it  
is set up within Jmol's WebExport only for changing background color.   
However, as soon as we finish debugging (mostly MSIE issues, which I  
think Angel has figured out), I will make the javascript available on  
my web site and in the Wiki.  The functions are set up so you can pass  
any script command with the color the user picks from the popup  
inserted in the appropriate place. It works a lot like jmolMenu or  
jmolButton. I think we are only a few days away from this.

Jonathan
On Jun 15, 2010, at 10:08 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 3
 Date: Mon, 14 Jun 2010 23:32:47 +0200
 From: Angel Herr?ez angel.herr...@uah.es
 Subject: Re: [Jmol-users] Coloring A molecular dynamically
 To: jmol-users@lists.sourceforge.net
 Message-ID: 4c169fff.26164.102c9...@angel.herraez.uah.es
 Content-Type: text/plain; charset=US-ASCII

 Jay,

 There are many wasy you can do that. Several parts:

 1. How to pick the color. Simplest is e.g. to have a select  
 control (a drop-down menu) with
 a few colors. The user selects one, the color value is passed to a  
 javascript variable that will
 later be fed to a Jmol script.
 A more sophisticated pick could use Jonathan's new widget, but it is  
 not yet prepared for that,
 only for background color. Easy to adapt, anyway.

 2. How to select the amino acid sequence. Maybe the user types it in  
 a textbox (input
 type=text). You read that using javascript. Then you can probably  
 use JmolScript select
 WITHIN(sequence, atomExpression) command with that.
 http://www.stolaf.edu/academics/chemapps/jmol/docs/#atomexpressions

 Other ways to set the sequence may be available.

 3. Apply the color. That's trivial.


 If you need help implementing this, please come back with a specific  
 example page.




  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Animations of Gaussian Geometry Optimization

[Jonathan Gutow]

Mike,

As Angel said, Jmol loads the Gaussian .log fine.  My recollection is that the 
Gaussian files contain all the steps in the optimization just like GAMESS (the 
package, I'm most familiar with).  Once the .log file is loaded all you should 
have to do is turn animation on with a script command.  Try frame rewind; 
animation on;.  If each step is in multiple files you will have to load them 
into frames separately, before starting the animation.  In the Jmol application 
you can just use the animation buttons up in the tool bar, to control the 
animation.  The development version of Jmol (12.0) will also automatically 
generate a web page with animation controls using the WebExport function/dialog.

Jonathan


On Jun 15, 2010, at 5:29 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 2
 Date: Tue, 15 Jun 2010 11:00:33 -0500
 From: Michael Evans evan...@illinois.edu
 Subject: [Jmol-users] Animations of Gaussian Geometry Optimization
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktilyrj9nkveug3q-6tqppjgz4vlcce9toopr5...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Lords of Jmol: I came across an interesting question the other day. A
 student wants to use Gaussian .log output to build an animation of the
 geometry minimization process from Gaussian's point of view, with each frame
 corresponding to a different geometry until the optimized structure is
 reached. Any thoughts on the best way to do this?
 
 Cheers and thanks, Mike
 
 -- 
 Mike Evans
 Organic Chemistry Graduate Student
 Moore Group
 University of Illinois, Urbana-Champaign

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] Is there a way to force a javascript function to execute after all applets have loaded?

[Jonathan Gutow]

Ah ha!  appletInfo.registry may be just the ticket.  However, I found  
a mistake in my code where I was updating my list of applets twice,  
that was causing my apparent mixing of applet IDs and callback  
messages.  So the simple message call back activated in a javascript  
... command works fine.

Thanks for the ideas.  I still may have occasion to use them with  
SAGE.  There is a tremendous amount of sever-browser traffic that  
can mess things up.  I may need other checking routines.

Jonathan
On Jun 14, 2010, at 12:02 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 The appletInfo.registry property also indicates all applets loaded  
 -- not
 just for the current page, but for all pages. The long number is a  
 random
 number that is associated with a specific page. The current page's  
 ID is
 found by checking _jmol.params.syncId.

 jmolGetPropertyAsArray(appletInfo.registry,)

 appletInfo.registry={}
 appletInfo 
 .registry 
 .jmolApplet0__246834263019686__ 
 =JmolApplet[panel0,0,0,350x350,layout=java.awt.FlowLayout]

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Java exception

[Jonathan Gutow]

Phil,

This is a problem specifically with how Mozilla browsers on the Mac pass local 
paths.  This has been a problem for years.  For local running of pages on a Mac 
you need to use a different browser.  The issue is that the Mozilla browsers 
insist on passing absolute paths through the javascript.  This causes a 
security exception when running locally.  Mozilla browsers work fine from the 
web.  I don't think we've ever tried to report this as it isn't an issue for 
pages from servers.

Maybe we need to add something to the Wiki.  The information is included in my 
WebExport tutorial in the section on testing locally.  

Jonathan
On Jun 8, 2010, at 12:03 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 5
 Date: Mon, 7 Jun 2010 18:16:44 -0400
 From: Philip Bays pb...@saintmarys.edu
 Subject: [Jmol-users] Java exception
 To: Jmol Jmol jmol-users@lists.sourceforge.net
 Message-ID: af61ccbf-6844-46a5-8631-c8d22c5fa...@saintmarys.edu
 Content-Type: text/plain; charset=us-ascii
 
 For a number of years I have had a series of tutorials that students have 
 successfully used.  I was using a pretty old version of Jmol and  recently 
 updated the website, incorporating a newer version (11.8.24).  The tutorials 
 using Jmol work fine on the Mac for all browsers except Mozilla (Firefox, 
 Camino, Seamonkey).  On these browsers the applet loads and the first 
 structure is shown.   However, subsequent reloads of the applet fail. They 
 fail completely on windows machines with Firefox but run with IE.  In the 
 Firefox applet window on the mac I get the statement:
 
   java.security.AccessControlException: access denied
 
 The Java console gives a permissions error as shown below.
 
 FileManager.getAtomSetCollectionFromFile(Acyclic/M4/S.pdb) //Acyclic/M4/S.pdb
 FileManager opening 
 file:/Users/pbays/Sites/Programs/Stereochemistry/Acyclic/M4/S.pdb
 file ERROR: file:/Users/pbays/Sites/Programs/Stereochemistry/Acyclic/M4/S.pdb
 java.security.AccessControlException: access denied (java.io.FilePermission 
 /Users/pbays/Sites/Programs/Stereochemistry/Acyclic/M4/S.pdb read)
 openFile(Acyclic/M4/S.pdb): 275 ms
 eval ERROR: java.security.AccessControlException: access denied 
 (java.io.FilePermission 
 /Users/pbays/Sites/Programs/Stereochemistry/Acyclic/M4/S.pdb read)
 
 load  Acyclic/M4/S.pdb 
 
 Any quick clue as to what is happening and what changed?  FYI: I did try 
 12.0RC12 and it behaved the same way.
 
 Phil 
 
 
 J. Philip Bays
 Professor of Chemistry
 Department of Chemistry and Physics
 Saint Mary's College
 Notre Dame, IN 46556
 (574) 284-4663
 pb...@saintmarys.edu
 



 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-users] New Feature: Simple Widgets now available in WebExport...

[Jonathan Gutow]

Dear Users:

The following simple widgets are now available to add to pages created by 
WebExport (the automatic web page generation):
1) Spin on/of checkbox
2) Background color picker with a color pallet to select from.
3) Animation control (icon buttons for mode plus play, stop, forward one and 
back one).
4) Open console button
5) Stereo viewing mode menu.
(more are coming...select vibrations, select MOs, color selected atoms or 
residues...)

Except for the Animation control and the Background color picker these 
essentially duplicate functionality in the pop-up menu.

We now have a relatively straightforward way of adding new widgets, so send in 
your requests!  I can't promise all of them, but I promise to do my best.

Jonathan


Note to translation team:  I updated the the .html help files associated with 
WebExport to reflect these widgets (see org.openscience.jmol.webexport.html).  
Thus translations need to be updated as well.  You will also see a few new 
pieces of vocabulary coming through the gettext system.

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[Jmol-users] Is there a way I can pick up the appletdestroyed message using javascript?

[Jonathan Gutow]

Hi all,

A javascript question.  Is it possible to pick up  the notification  
that one of the Jmol applets on my page has been destroyed  in  
javascript?  I know I've seen a message to that effect somewhere.

Thanks,
Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Is there a way I can pick up the appletdestroyed message using javascript?

[Jonathan Gutow]

Thanks.  I'll give that a try.  I'm trying to keep track of div's that have 
their contents destroyed by the server in SAGE without having to plug into the 
server communication interface since that is in flux.

Jonathan
On Jun 3, 2010, at 5:06 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Message: 3
 Date: Thu, 3 Jun 2010 17:05:32 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Is there a way I can pick up the
   appletdestroyed message using javascript?
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktim2fpxunuq8jliwlasv6fyhxgdgp_sdobujw...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 the message goes to the Java console only, not out to the web page. i think
 you can just check with:
 
 if (!document.getElementById(jmolApplet0)) 
 
 how do they get destroyed if you are still on the page?
 
 Bob

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Re: [Jmol-users] Jmol radio ui works, but no result

[Jonathan Gutow]

Jay,

What machine are you testing it on.  There was a bug in the MacOS 10.6 JVM that 
was causing problems with execution of script calls using the javascript  
interface.  It seems to have been fixed in the latest update.  If you are using 
a Mac and a webkit browser for testing make sure you are using java 1.6.0_20, 
not 1.6.0_17.  You can check this in the System part of the Jmol popup menu.

Jonathan
On May 23, 2010, at 2:17 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 From: Jay Vyas jayunit...@gmail.com
 Subject: [Jmol-users] Jmol radio ui works, but no result
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktikron_8r5otu5sisho5btxwelihizlvqmme8...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Hi Guys :
 
I have an application that uses JMol, but the radio controls wont
 trigger any events.
 Im puzzled because :
 
 1) I dont see any errors in the java script console.
 
 2) The JMol Console is clearly registering the events associated with the
 buttons...
 
 But alas, there is no result in the rendering of my molecule.
 
 Below is the Code for this page.  I've truncated the structure info so
 as to make this email
 less than the size of the TrpRepressor crystal structure's pdb file ;)

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[Jmol-users] getting script error on new example topic 135 (sculpt)

[Jonathan Gutow]

I'm now getting this script error when I try to run the example.

script ERROR: unrecognized SET PICKING SELECT parameter: dragminimize  
 set picking  dragminimize 
10:30 CDT
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] getting script error on new example topic 135 (sculpt)

[Jonathan Gutow]

Something like that.  Oddly it required a complete reboot.  Maybe my  
javaVM got mangled in RAM.

And Yep, this is cool.  This makes me think again about using the UFF  
and an easier to specify rotation of a group to do simple energy plots  
for rotation about a single bond...Still thinking about the interface  
though...

Jonathan
On May 21, 2010, at 12:13 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] getting script error on new example topic
   135 (sculpt)
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktilxymfcuej9xeniw2ub7ekfxj1k4eqxhztl6...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Some kind of caching problem on your end, I think. Close your  
 browser and
 reopen it.

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] e: ah, this is very, ah, WEIRD--error messages

[Jonathan Gutow]

I have the same problem as phil.  It seems to be browser independent.  Here's 
the error messages.

Exception in thread AWT-EventQueue-2 java.lang.NullPointerException
at org.jmol.viewer.Viewer.getSelectionHaloEnabled(Unknown Source)
at org.jmol.viewer.Viewer.getBooleanProperty(Unknown Source)
at org.jmol.popup.JmolPopup.show(Unknown Source)
at org.jmol.viewer.Viewer.popupMenu(Unknown Source)
at org.jmol.viewer.ActionManager.mousePressed(Unknown Source)
at org.jmol.viewer.MouseManager14.mousePressed(Unknown Source)
at org.jmol.viewer.MouseManager14.mousePressed(Unknown Source)
at java.awt.Component.processMouseEvent(Component.java:6345)
at java.awt.Component.processEvent(Component.java:6113)
at java.awt.Container.processEvent(Container.java:2085)
at java.awt.Component.dispatchEventImpl(Component.java:4714)
at java.awt.Container.dispatchEventImpl(Container.java:2143)
at java.awt.Component.dispatchEvent(Component.java:4544)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
at 
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at 
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

Clearing out all the caches and restarting browsers doesn't help.  Nor does 
choosing to run the applet as its own process.

Jonathan


On May 20, 2010, at 7:33 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 so you don't even see a structure?
 
 On Thu, May 20, 2010 at 7:07 PM, Philip Bays pb...@saintmarys.edu wrote:
 
 Bob:
 
 I click on the red text in the description which transfers the command to
 the command area under the applet.  Clicking on cmd results in nothing.
 (Mac 10.6.3, java 1.6 something.)
 
 Phil

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Re: [Jmol-users] RC9-11 nonstarters?

[Jonathan Gutow]

I can verify this observation.  It doesn't work with java version 1.5,  
at least on MacOSX 10.5.8.  I'm suspicious that we have something that  
requires 1.6, as my machine with java 1.6 works.  Can anybody find a  
java 1.5 machine where it does work?  I do think we need to support  
1.5 as that is still considered a supported version.

Jonathan
On May 18, 2010, at 7:35 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 To check the java version just open up a terminal
 (Application-Terminal) and type

 java -version

 The version on my work machine is

 java version 1.5.0_22

 and that failed with the error messages I quoted.

 Rich

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] RC9-11 nonstarters?

[Jonathan Gutow]

Looks OK.  The applet works fine on the machine that RC12 application  
will not open on.  The Java version used for the applet plugin is  
1.5.0_22 just as for the application.  Mac OSX 10.5.8

Jonathan
On May 19, 2010, at 10:22 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Wed, 19 May 2010 10:22:48 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] RC9-11 nonstarters?
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   aanlktikbkx0gzukbxqa02oi3vnj3a-fnrrrpatvjd...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Jonathan, I'd like to make this a high priority. One thing I notice  
 is that
 Java 1.5 has the annoying characteristic to ask if you really want  
 to run an
 applet intended for an older version of Java. I guess they figured  
 out that
 that was a dumb idea, because it is not there in 1.6. So I believe  
 the only
 issue should be with 1.5, and it could be just this -- that by  
 setting the
 target version to 1.4, this triggers a bug in Java 1.5 on the Mac  
 that
 makes it not work. I don't know. But it works fine with Java 1.5 on  
 the PC.

 Another possibility is that the particular Java 1.5 that people are  
 using
 has that bug.

 My main concern is that the APPLET works. So please do check that  
 the applet
 is working for you. The one I have up now on the web at my site is  
 compiled
 with a target 1.4 and runs just fine on my machine when I use Java  
 1.4 for
 the browser Java.

 Thanks,

 Bob

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] RC9-11 nonstarters?

[Jonathan Gutow]

12.RC12 works fine for me when I compile from source on MacOS X 10.6.3.

However, it does not launch when I try to launch the downloaded .jar  
on 10.5.8 JSE 5.0.
I'll have to get home to try it on 10.6.3 from download.

The error involves a version number problem.  I suspect it relates to  
the recent change in the required java version.  Something is not  
consistent.  Here is the log of the error messages. Sorry for the very  
long lines, but that is what the system console generates.

Eric, you've definitely found something.

Jonathan

May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]: Exception
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]: in thread main
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  
java.lang.UnsupportedClassVersionError: Bad version number in .class  
file
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.lang.ClassLoader.defineClass1(Native Method)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.lang.ClassLoader.defineClass(ClassLoader.java:676)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.net.URLClassLoader.access$100(URLClassLoader.java:56)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at java.net.URLClassLoader 
$1.run(URLClassLoader.java:195)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.security.AccessController.doPrivileged(Native Method)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.net.URLClassLoader.findClass(URLClassLoader.java:188)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.lang.ClassLoader.loadClass(ClassLoader.java:317)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at sun.misc.Launcher 
$AppClassLoader.loadClass(Launcher.java:280)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.lang.ClassLoader.loadClass(ClassLoader.java:252)
May 18 15:34:36 Chem-MacBook-Pro-Gutow  
[0x0-0xe80e8].com.apple.JarLauncher[3433]:  at  
java.lang.ClassLoader.loadClassInternal(ClassLoader.java:375)



On May 18, 2010, at 2:25 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Tue, 18 May 2010 15:25:18 -0400
 From: Philip Bays pb...@saintmarys.edu
 Subject: Re: [Jmol-users] RC9-11 nonstarters?
 To: jmol-users@lists.sourceforge.net
 Message-ID: 0de771da-4568-43e3-b540-5dbb1abae...@saintmarys.edu
 Content-Type: text/plain; charset=us-ascii

 Sorry about that.  But 12.0.RC12 Jmol.Jar lunches fine for me.


 On May 18, 2010, at 2:32 PM, Eric Martz wrote:

 Thanks for the report, but what I need someone to test on OS X is
 12.0.RC12 (or RC11). I just downloaded RC12 and it too fails to
 launch. Tests of RC12 Jmol.jar on Windows would also be welcome.  
 Thanks, -Eric

 At 5/18/10, Philip Bays wrote:
 MacBook Pro running 10.6.3.
 I downloaded RC 11.9.36 and Jmol.jar launches just fine.   I did not
 play with it.

 Phil

 On May 18, 2010, at 10:22 AM, Eric Martz wrote:

 I did three separate downloads for RC9, RC10, RC11. None worked. At
 the same time, I downloaded 11.8.24 and it worked. So I don't think
 it was a random corrupted file. Can someone else using a Mac please
 try the *application* from RC11? -Eric


  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] RC9-11 nonstarters?-location of java start up errors...

[Jonathan Gutow]

Eric,

On the Mac the java startup error information goes to the system console.  Just 
open the console application available in the Utilities directory which is 
usually inside the Applications directory.

Jonathan
On May 18, 2010, at 4:16 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Date: Tue, 18 May 2010 17:13:30 -0400
 From: Eric Martz ema...@microbio.umass.edu
 Subject: Re: [Jmol-users] RC9-11 nonstarters?
 To: jmol-users@lists.sourceforge.net
 Message-ID: 201005182113.o4ildafs010...@marlin.bio.umass.edu
 Content-Type: text/plain; charset=us-ascii; format=flowed
 
 Thanks to you and Jonathan. How do you get the Java console error 
 messages? I am also running OS 10.5.8. When I attempt to launch 
 Jmol.jar, the console never shows up. When I have another version of 
 Jmol.jar or the applet running, I can access a Java console, but no 
 error messages appear.
 
 Just curious. -Eric

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Re: [Jmol-users] MO display problem

[Jonathan Gutow]

Verified on MacOS, Firefox 3.6.3 Java 1.5.0_22, you are using  
Jmol12.0.RC6 (is that right).

That is weird looking.  I can also get it to happen when rotating by  
hand.  It looks as if the frame is changing, but it doesn't appear to  
be.

It does not appear to happen when the mo is created using the  
isosurface command:

isosurface modelmo mo 1

Jonathan
On Apr 21, 2010, at 1:50 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 1
 Date: Tue, 20 Apr 2010 12:35:35 -0400
 From: Otis Rothenberger osrot...@chemagic.com
 Subject: [Jmol-users] MO display problem
 To: Jmol Users jmol-users@lists.sourceforge.net
 Cc: Tom Newton new...@usm.maine.edu
 Message-ID: 4bcdd7d7.2010...@chemagic.com
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 In Jmol 12.0.RC6_dev, I'm seeing peculiar behavior of MO's. Once
 displayed, the MO's disappear and reappear at various positions during
 mouse rotation or the spin command.

 The script

 load ../meps/alkene!1-butene_mo.mol;mo 1;spin

 in the script text field (followed by clicking Run) on the following
 page will illustrate the problem:

 http://chemagic.com/web_molecules/script_page_large.aspx

 Has anyone else seen this problem? I don't think it is related to  
 other
 code on the page.

 Otis

 -- 
 Otis Rothenberger

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Want some opinions on rotation about bond before posting a feature request...

[Jonathan Gutow]

Dear Jmol Users,

One of my colleagues asked for an easier way to do rotation about a  
bond than selecting the atoms in a group and then using  
rotateSelected {ID of atom 1 of bond} {ID of atom 2 of bond}.  They  
would like some kind of a GUI interface that students could use.  I  
think clicking on atoms to select them is OK.  It is having to use the  
command that is a problem.  Any thoughts on how this should work?   
There is something working in a recent version of RasMol according to  
this colleague. Avogadro and Spartan also have relatively elegant ways  
of doing this.  Once a general consensus is reached I will add it to  
the feature request list.

Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Want some opinions on rotation about bond before posting a feature request...

[Jonathan Gutow]

Otis,

Your thoughts are helpful. Your comments on needing to click on two  
atoms to select the bond, suggests to me that if we could accept bond  
selection by clicking in the middle of the bond, you think it would be  
better.

My colleague is looking for something that works inside the  
application not on a web page.

So here's what I'm thinking so far (to be implemented in the  
application and in some way in the applet as well):

1) The user selects a group of atoms by clicking on the atoms.
2) The user selects a bond to rotate the group about by clicking the  
center of the bond (ideally) or selects the bond by clicking on either  
end (this will require some way of telling the program that this is a  
bond selection).
3) The rotation  group is set to just be the selected atoms so the  
normal mouse drag can be used for the rotation.

Does that sound good?

Jonathan
On Apr 14, 2010, at 12:44 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 4
 Date: Wed, 14 Apr 2010 13:43:25 -0400
 From: Otis Rothenberger osrot...@chemagic.com
 Subject: Re: [Jmol-users] Want some opinions on rotation about bond
   before posting a feature request...
 To: jmol-users@lists.sourceforge.net
 Message-ID: 4bc5febd.60...@chemagic.com
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 Hi Jonathan,

 I'm working on this right now. Currently, we use unbind and bind to
 allow mouse rotation and translation of separate models in a Jmol
 window. In the same application, we use the two atom click system that
 you mention for bond rotation definition. This is followed by the need
 to click a rotate button. I'm trying to use the same logic that we use
 with the independent movement of molecules via mouse movement. I think
 it's doable.

 While the feature (independent movement of two model) must be turned  
 on
 and off, it's painless once it's on. A hover callback does all the
 required selection. That's the part of the code that I'm working on  
 now
 for bond rotation. Writing an appropriate hover callback for the bond
 rotation. I will say that so far I see no way around the two atom  
 click
 definition of the bond axis. If anyone has an idea of how a hover
 callback could define this, please send suggestions. In the case of
 using hover to define (select) one or the other model of a two model
 system, it's pretty easy. They are not connected. For a single  
 connected
 system, hover could select the hovered atom and maybe even pick up the
 required second atom, but subsequent mouse movement could easily screw
 up these selections.

 Otis

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Please clean up messages when replying to the list...

[Jonathan Gutow]

I would like to request that people please clean out the nested quotations when 
they reply to the list.  It is reasonable to keep the pertinent information 
that is being commented upon, but usually multiple nested replies are just 
wasting bandwidth.  They also make it more difficult for those who scan 
digested versions to find the pertinent information.

Thanks,
Jonathan
On Apr 10, 2010, at 9:11 PM, jmol-users-requ...@lists.sourceforge.net wrote:

 Send Jmol-users mailing list submissions to
   jmol-users@lists.sourceforge.net
 
 To subscribe or unsubscribe via the World Wide Web, visit
   https://lists.sourceforge.net/lists/listinfo/jmol-users
 or, via email, send a message with subject or body 'help' to
   jmol-users-requ...@lists.sourceforge.net
 
 You can reach the person managing the list at
   jmol-users-ow...@lists.sourceforge.net
 
 When replying, please edit your Subject line so it is more specific
 than Re: Contents of Jmol-users digest...
 
 
 Today's Topics:
 
   1. Re: Jmol Virtual Model Kit (Otis Rothenberger)
   2. Re: Jmol Virtual Model Kit (Robert Hanson)
 
 [snip]
 
 
 End of Jmol-users Digest, Vol 47, Issue 17
 **


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[Jmol-users] Another publication about Jmol...

[Jonathan Gutow]

J. Chem. Ed. has just published a brief description of Jmol and the  
export to web function as well as archived a copy of the tutorial I  
put together.  I'll add the link to the Wiki, but post it here in case  
anybody cares.

J. H. Gutow, Easy Jmol Web Pages using the Jmol Export to Web  
Function   Journal of Chemical Education WebWare.  Publication Date  
(Web): April 8, 2010.
link: http://pubs.acs.org/doi/abs/10.1021/ed100283v

Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Some examples of what my students are doing with Jmol...

[Jonathan Gutow]

In case anyone is interested my P-Chem students have made Jmol based web 
presentations on their attempts at quantum calculations .  I haven't graded 
them yet and suspect they all have some problems with explanation, but the Jmol 
parts work.  If you want to look, follow the links to the quantum web reports 
in the 4/3/10 announcements on this page.

http://www.uwosh.edu/facstaff/gutow/copy_of_physical-chemistry-1/p-chem-1-home

Jonathan

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Re: [Jmol-users] visualizing potential energy surfaces...

[Jonathan Gutow]

Bob,
I think Peter is thinking about the things we discussed for making  
Jmol into a general nD function plotter/slicer.  I haven't had much  
time to think about it, but I believe we left off discussing the issue  
of rotations in 3D.  The simplest implementation is just to only  
display a surface defined by a triplet of values (x  y as coordinates  
and z as the potential/total energy, while choosing a fixed value for  
each of the left over coordinates). Depending on how the coordinate  
grid is specified this might require some interpolation.

Peter, is this what you are thinking of?

Jonathan
On Apr 1, 2010, at 2:01 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 4
 Date: Thu, 1 Apr 2010 14:00:55 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Visualising potential energy surfaces
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   x2hba9c0bd61004011200we2bf72b5ha8d7e5ecce87f...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Peter, good to hear from you!

 I'm not sure what a potential energy surface is, exactly.  
 Generally when
 people say they want to display potential they mean electron  
 potential --
 just mapping electron potential onto electron density. It simply  
 requires
 two sets of volumetric data. If the electron density is not used,  
 then the
 VDW surface can be used (isosurface sasurface 0).

 But maybe this is something else?

 Bob

 On Mon, Mar 29, 2010 at 7:28 AM, Peter Murray-Rust pm...@cam.ac.uk  
 wrote:

 I have met a participant (Bcc'ed) at the Trieste Workshop on  
 Molecular
 computation on the GRID who is interested in whether Jmol can display
 potential energy surfaces. AFAIUI this means sets of multidimensional
 points, each with an energy. (Obviously only 3 dimensions can be  
 displayed
 in Jmol but perhaps it would be possible to select between different
 views). Has anyone looked at visualising f(w,x,y,z... surfaces)?

 P

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Brian McMahon's talk at ACS meeting was good publicity for Jmol...

[Jonathan Gutow]

Brian,
You don't know this, but I got to attend your talk on Interactive  
publishing of structure data (I asked the last question about the  
signed applet:), hope that was OK).  I just wanted to publicly thank  
you for the good publicity for Jmol.

I also wanted to put in a plug for others to look at the publishing  
interface the International Union of Crystallography has developed and  
encourage other journals to emulate it.  It looks like the best  
submission system I have yet seen.

One other point that you made in your talk that is very important long  
term.  We need to come up with a common language for describing 3-D  
views and manipulation.  Maybe the key players leading this   
discussion should be the IUCr and the PDB?  Is there a similar group  
that could provide representation for the quantum community?  Anybody  
else that should be included?

Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Singular Value Decomposition, was Jmol align

[Jonathan Gutow]

My favorite reference for algorithms is:
  _Numerical Recipies_ The old version I have on my bookcase is by  
Press, Flannery, Teukolsky and Vetterling.  It was published by  
Cambridge University Press.

Jonathan
On Mar 11, 2010, at 3:20 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 3
 Date: Thu, 11 Mar 2010 10:42:45 -0600
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Jmol align
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   ba9c0bd61003110842i22fe3759pe9854c0b9acdb...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 I think I can do it with quaternions in about two lines of Jmol  
 script. Is
 there a good reference for Singular Value Decomposition?

 Bob

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Poll of favorite/most important new Jmol features (I'm giving a presentation)...

[Jonathan Gutow]

Dear Jmol Users:

I will be giving a presentation primarily on using the export to web  
function of Jmol  in a classroom setting at the upcoming National  
American Chemical Society meeting.  I cannot devote much time to it,  
but wanted to present some Jmol's features and how it is evolving in  
my introduction.  Thus I would like people to post lists of their  
favorite/most important new features (say in the last year or so).  I  
will use this to inform what I include in my introduction.

Thanks,
Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Mac Question re unbind/bind

[Jonathan Gutow]

Otis,
This issue may be that the system binds cntrl-left = right mouse  
button.  This is because until recently most macs came with a one  
button mouse.  I always replaced it with a two-button/scroll-wheel  
mouse:). But on my mice the cntl-left still brings up the context  
sensitive right button menus.  My guess is your unbind is only  
affecting the browser, so everything is captured by the OS and you  
don't get signal passed through.

Jonathan
On Mar 4, 2010, at 1:05 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 3
 Date: Thu, 4 Mar 2010 13:30:44 -0500
 From: Otis Rothenberger o...@chemagic.com
 Subject: [Jmol-users] Mac Question re unbind/bind
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   daf3612f1003041030y703525ady7cbc7981a1bf8...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Hello,

 I'm using the following start up script to unbind and bind CTRL  
 operations:

 unbind 'CTRL-LEFT'; bind 'CTRL-LEFT' 'rotateSelected Y
 _DELTAX;rotateSelected X _DELTAY;';unbind 'CTRL-RIGHT'; bind 'CTRL- 
 RIGHT'
 'translateSelected {_DELTAX/100 _DELTAY/-100 0};'

 Under Windows, the script works with Firefox, MSIE, and Chrome.  
 Under Mac
 (Firefox and Safari), I am getting user reports that the translation  
 works,
 but the rotation does not. Specifically, the unbind of CTRL-LEFT  
 seems to
 work, but the bound script does not work. The assessment that the  
 unbind is
 working is based on the fact that CTRL-LEFT does nothing. It should, I
 think, raise the Jmol menu, so it seems to be properly disconnected  
 by the
 above script.

 Three questions:

 1. Does anyone see a problem with my rotation script? I should note  
 that the
 rotateSelected Y _DELTAX format is intentional.

 2. Is there anything special about CTRL-LEFT on a Mac that might  
 interfere
 with this?

 3. I don't have convenient access to a Mac, can anyone easily swap  
 LEFT and
 RIGHT in the above script to check if the swap moves the problem to  
 the
 translate and fixes the rotate? The following page has a command  
 field that
 could check this:

 http://chemagic.com/web_molecules/script_page_large.aspx


 Otis

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Bugs in 11.9.29

[Jonathan Gutow]

On Feb 13, 2010, at 10:57 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 With current Apple java 1.5.0_22, you can no longer block, drag and drop
 the state script (and forever you can't copy and paste it). Yikes!
 
 
 Be sure to report that -- a major Java bug.
Actually, you can copy and paste using cntrl-C and cntrl-V instead of the 
standard cmd-C and cmd-V in MacOS.  This is not a Java bug, but due to the fact 
that we do not use the swing look and feel wrapper that would switch buttons 
etc to look and behave more mac-like.  I'm not sure if that would  make a 
difference for the applet anyway.

Jonathan

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Re: [Jmol-users] UI preference question (WebExport Dialog)...

[Jonathan Gutow]

Angel,
I'm not sure I understand this objection.  As I've got it working in  
my test case this is what happens:
1) When the user selects a single instance in the webexport list of  
instances, the viewer reloads that instance.  Nothing happens if  
multiple instances are selected.  This is the same behavior as  
clicking on the show selected instance button.
2) If you delete the instance you still have it in the viewer and can  
add it back if that was a mistake.  It acts as sort of a an undo  
delete, which we don't have at present.  I'm actually wondering  
whether we should have an undo delete for deletion of multiple views.
3) The reason I started trying this is that it was a one line addition  
after I fixed the dimension spinners to reflect show the dimension of  
each instance applet as it is selected.  Also added the ability to  
change the dimensions without having to re-add the instance to the list.

Downsides I see:
If the setup of the view is complicated it can take a while for the  
viewer to update.
If you've made a new view and want to keep it, but haven't added it to  
the list it will disappear. (Is this what you're worrying about, Angel?)

Do we need a separate mini-viewer for the instances in the list?...I  
think that would make the interface complicated for the user...Thoughts?

Upsides
automatic undo for single deletions
user gets feedback on what the view/instance looks like, without  
having to ask for it.


On Feb 8, 2010, at 3:03 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Mon, 8 Feb 2010 11:03:04 +0100
 From: Angel Herr?ez angel.herr...@uah.es
 Subject: Re: [Jmol-users] UI preference question (WebExport Dialog)...
 To: jmol-users@lists.sourceforge.net
 Message-ID: 4b6fe158.17810.2f0...@angel.herraez.uah.es
 Content-Type: text/plain; charset=US-ASCII

 I don't think so, Jonathan. Better to have such thing done
 consciously.
 Also, if I want to delete a view from the list, I must select it
 first. If the view in Jmol changes automatically, then I've lost the
 view I had in favour of one I do not want to keep.

 I think it is OK as it is now.

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] UI preference question (WebExport Dialog)...

[Jonathan Gutow]

On Feb 9, 2010, at 10:39 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:


 Nothing happens if
 multiple instances are selected.

 Nothing? The first selected one will be displayed, right?

Oops!  Yes, the first item clicked on is displayed.

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] UI preference question (WebExport Dialog)...

[Jonathan Gutow]

In the WebExport Dialog we presently have a button you must click to  
make the selected view (instance) show up in the viewer window.  Would  
people prefer to have this happen when the view is selected in the list?

Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] GUI color picker updates...try them and comment...

[Jonathan Gutow]

On Jan 13, 2010, at 10:59 AM, Angel Herr?ez wrote:

 The color picker looks great. One possible addition would be to use a
 more suggestive icon rather than the little table: a palette maybe?
 http://commons.wikimedia.org/wiki/File:Nuvola_apps_kcoloredit.svg
Yeah, that bothered me too.  I've put up another version that uses a  
little pop-up menu arrow and has the look of the chooser a little  
better too.
http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol%20Color%20Picker%20Test.html
I've also put together a more general colorpicker not tuned for Jmol.
http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Test%20VSColorPicker.html

 Maybe you didn't notice there was already some effort into this by
 S?rgio Ceroni:
 http://wiki.jmol.org/index.php?title=Recycling_Corner#Molecule_color_p
 icker
I did look at that as I designed this one.

Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] GUI javascript color picker widget for Jmol, please look at and vote on inclusion in Jmol.js...

[Jonathan Gutow]

I think that's a good idea.  We would need to rewrite this into Java  
rather than javascript.  But I see no reason it couldn't be done.

Jonathan
On Jan 5, 2010, at 10:03 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Mon, 4 Jan 2010 14:54:51 -0800
 From: Thomas Stout thomasjst...@gmail.com
 Subject: Re: [Jmol-users] GUI javascript color picker widget for Jmol,
   please  look at and vote on inclusion in Jmol.js...
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   75750581001041454k4c424321pf315a634a40f8...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Oh!  I meant to have the whole dealie embedded within the Jmol  
 applet 
 accessed through a pop-up window/menu, rather than in the html  
 portion of
 the web page --  I guess that is what would happen if it were  
 incorporated
 into Jmol.js??

 -Tom

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] GUI color picker updates...try them and comment...

[Jonathan Gutow]

I've changed the javascript colorpicker based on some people  
comments.  There is now a bar at the top that flashes the color you  
are hovering over and an X in a box to cancel choosing a color.

Let me know what you think.

Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] A more versatile minimalist ColorPicker from J Gutow...

[Jonathan Gutow]

In the process of developing the color picker box for Jmol I also came  
up with a somewhat more adaptable color picker, for testing  
purposes.   It can vary size and resolution each time it is called.   
Anything with a background color on the page below has a colorpicker  
attached to it.  Just click to activate.

Jonathan

http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Test%20VSColorPicker.html

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] GUI javascript color picker widget for Jmol, please look at and vote on inclusion in Jmol.js...

[Jonathan Gutow]

On Jan 4, 2010, at 2:55 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Mon, 4 Jan 2010 12:55:50 -0800
 From: Thomas Stout thomasjst...@gmail.com
 Subject: Re: [Jmol-users] GUI javascript color picker widget for Jmol,
   please  look at and vote on inclusion in Jmol.js...
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   75750581001041255q3c4413b8s6a3ea5b69c40e...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 I think this would make a very useful addition to Jmol!  Is there a  
 way to
 vote +1 ?!  :)
Tom,
Thanks!

 One thought for future implementation: I would love to utilize it as a
 pop-up color selection menu/window, so that it's there when needed  
 but not
 occupying screen space other times...
Not sure what you mean here.  Do you want something smaller than the  
two little squares that the colorpicker pops up from?  I have thought  
about a more general color picker that is not specific to Jmol, is  
that what you want?

Jonathan

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] GUI javascript color picker widget for Jmol, please look at and vote on inclusion in Jmol.js...

[Jonathan Gutow]

Dear Jmol Users:

(What I did on my holiday break...:)) As part of my work on the Jmol  
interface for the SAGEmath project, I have put together a color picker  
box that pops up a palette of colors to choose from and then passes  
the user's choice into a Jmol script which is then passed to the  
applet.  I don't think it would take much more effort to make this  
work as part of Jmol.js.  However, before I and possibly other people  
put any effort towards that, I wanted to find out if the Jmol  
community thinks this is something they would use.

Please take a look at the example page showing the color picker box in  
action to see what I'm talking about:

http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol%20Color%20Picker%20Test.html

Then please vote directly to this list with a

yes or +1 (for you would like to see it included)

or

no  or -1 (for you can't see a use for this)

Also comments about how it looks or functions would be useful.

Then I and other people working on Jmol development can decide how  
much more effort to put towards this.

Thanks,
Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] GUI javascript color picker widget for Jmol, please look at and vote on inclusion in Jmol.js...

[Jonathan Gutow]

From: Robert Hanson hans...@st... - 2010-01-03 02:45
 Nice! Let's see if we can tighten that code up a bit

Thanks.  It definitely needs some work.  A couple of things that  
glaringly need to be fixed if this is to become part of Jmol.js: 1)I  
haven't extracted everything I had to put in to work around the  
asynchronous nature of the SAGE server (although I think I've got most  
of it); 2) I am not using all the facilities already included in  
Jmol.js, especially some of the things done to handle older browsers;  
3) I've only tested it well with FireFox and Safari, so far.  I also  
think we may want to consider changing the syntax a little to match  
other Jmol.js function calls better.

If the response continues to be positive, we should definitely work on  
this and move the code discussion to the developers list.

Jonathan

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Need help passing a state script form one applet to another via javascript...Got it!...

[Jonathan Gutow]

Everybody thanks for the advice.  I've got it working.  I did have to  
use the vertical line syntax, which I believe was implemented for  
inline data because of CR/LF problems sometime in the past. In the  
process, I've also managed to store the state data in a hidden div  
rather than a variable, which is important for me as, I believe, I can  
easily have that archived by a SAGEmath notebook server so that the  
page will open in the user adjusted state later.

Thanks again,
Jonathan
On Dec 19, 2009, at 7:57 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Fri, 18 Dec 2009 13:25:10 -0600
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Jmol-users Digest, Vol 43, Issue 29
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   ba9c0bd60912181125g4a73fa41me1fbdb61c659f...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 There's just something simple you are missing. Could be a Mac issue  
 with
 line endings. You might try to replace all \r characters with \n  
 characters.


 All my tests with similar state scripts work just fine.

 On Fri, Dec 18, 2009 at 12:50 PM, Jonathan Gutow gu...@uwosh.edu  
 wrote:

 Sorry I mistyped that the actual text from the returned state is

 data model inline
 10
 empty
 Xx -6.0 -7.0 -3.0
 Xx 0.0 -7.0 -3.0
 Xx 6.0 -7.0 -3.0
 Xx 7.0 -6.0 -3.0
 Xx 7.0 0.0 -3.0
 Xx 7.0 6.0 -3.0
 Xx -7.0 -6.0 -3.0
 Xx -7.0 -6.0 0.0
 Xx -7.0 -6.0 3.0
 Xx 5.5 5.5 5.5
 end model inline;;

 Which looks right to me, but doesn't work when passed.  I'm going to
 try parsing it to convert to the vertical line syntax for inline  
 data.

 Jonathan

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
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  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Need help passing a state script form one

[Jonathan Gutow]

Otis,
Thanks for the example.  However, I'm mystified as to the difference  
between using a message call back to get the state string and my use  
of jmolGetPropertyAsString...They should give the same result.  Have  
you ever used your method with an inline set of data?  My method works  
fine if that part of the script is deleted.

I'm pretty convinced the issue is CR/LF stuff.  The inline data  
parser uses line breaks to differentiate the different pieces of  
data.  The rest of the script parser separates statements with a semi- 
colon.  I am also still checking some things that might relate to   
marks, but don't think this is a problem as  marks work in the rest  
of the transferred script.

Jonathan
On Dec 18, 2009, at 8:16 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Fri, 18 Dec 2009 08:16:32 -0600
 From: Otis Rothenberger o...@chemagic.com
 Subject: Re: [Jmol-users] Need help passing a state script form one
   applet  to another via javascript...
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   daf3612f0912180616y65042fbdsab4fbe9f7497f...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Jonathan-

 Any ideas?


 I had exactly the same problem. I finally used the following approach
 to copy/paste state from one applet to another in Jmol 11.9.9. I do
 not use jmol.js, so some of the function calls may seem strange to
 you. Nevertheless, I think that the basic concept below is readable.
 One Note: Some time is needed between copy and paste. I use user
 lag time in making a transfer manually. For automatic transfer, you
 may need to use a JavaScript setTimeout delay between copy and
 paste.

 Use show state to pass state as a message:

 function copyMol() {
if (feedbackFlag) { feedback(r[9]); }  //  Relevant to my page  
 only.
evalRasmol(select *);  // My script eval function. Its name is
 obviously historic!
evalRasmol(show state;delay 2;);
mepsData[tempHold] = mepsData[jmol1];  // Relevant to my page  
 only.
 }

 Use message call back function to put state info into global  
 variable jmolVar1.
 Use a variable - not hidden field. Hidden fields gave me problems -
 probably CR/LF issues.
 They may be hidden, but they seem to insert platform specific line  
 info:

 function processMessage(appNum, messageString, indexNum) {
if (messageString.indexOf(function _setWindowState() {)  -1) {
 jmolVar1 = messageString + ; }
 }

 Put state info in new Jmol applet:

 function pasteMol() {
if (feedbackFlag) { feedback(r[9]); }  // Relevant to my page only.
evalRasmol(select *);
evalRasmol(jmolVar1);
 }

 Best Regards
 Otis

 -- 
 Otis Rothenberger
 http://chemagic.org

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Jmol-users Digest, Vol 43, Issue 29

[Jonathan Gutow]

Sorry I mistyped that the actual text from the returned state is

data model inline
10
empty
Xx -6.0 -7.0 -3.0
Xx 0.0 -7.0 -3.0
Xx 6.0 -7.0 -3.0
Xx 7.0 -6.0 -3.0
Xx 7.0 0.0 -3.0
Xx 7.0 6.0 -3.0
Xx -7.0 -6.0 -3.0
Xx -7.0 -6.0 0.0
Xx -7.0 -6.0 3.0
Xx 5.5 5.5 5.5
end model inline;;

Which looks right to me, but doesn't work when passed.  I'm going to  
try parsing it to convert to the vertical line syntax for inline data.

Jonathan
On Dec 18, 2009, at 10:25 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Fri, 18 Dec 2009 09:21:36 -0600
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Need help passing a state script form one
   applet  to another via javascript...
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   ba9c0bd60912180721t325d9ffcq7ae18c954e340...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Interesting. inline data is not a recognized data header. I'm  
 surprised
 Jmol is saving that in the state. What version of Jmol is this?  
 (Could be a
 difference with 11.8 vs. 11.6, I suppose.)

 generally to get the data you would use

 var data = jmolScriptWait(show data)

 Bob

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Need help passing a state script form one

[Jonathan Gutow]

Bob,
I'll send you the state privately so as not to clutter up the list,  
but I think my reply is pertinent to the list.  There is no model  
loaded only a model that was created inline in the initial  script  
(these are the atoms used to hang axis labels on...something you've  
just made obsolete!  Thanks).  So I think it is appropriate that they  
be included in the state.

Jonathan
On Dec 18, 2009, at 12:07 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Fri, 18 Dec 2009 10:27:09 -0600
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Need help passing a state script form one
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   ba9c0bd60912180827o53bbb28am5b3a8de6d0308...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Is the script coming from a save of the state? I don't see how Jmol is
 saving that data in the state, so I must be missing something. It is  
 not
 supposed to save data in the state.

 Send me the state.

 Bob

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] what is Jmol for?

[Jonathan Gutow]

As one of the developers at the interface of this work with SAGE I  
guess I should comment.

I agree that I would not like take away from the development of Jmol  
for 3-D chemical visualization.  However, I do not think that this  
work  is unrelated for a number of reasons:

1) I got involved because I use Jmol primarily in my teaching for  
standard molecular visualization and in SAGE for mathematical function  
visualization.  So, at least in my case, improving Jmol in SAGE is  
useful to a chemist.

2) Better handling of function graphing in 3-D and axis labeling would  
allow display of potential energy surfaces generated from ab initio  
calculations.  At present one needs to make the plots in specialized  
software and it is not easy to have a live plot on the Web.

3) As Bob has already said the changes so far have also benefited the  
display of more standard stuff such a molecular orbitals, protein  
pockets and such.

4) If there are things you want developed that we are not getting to,  
why not lend a hand?  Jmol is open source, after all.

Jonathan
On Dec 16, 2009, at 8:50 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Wed, 16 Dec 2009 17:35:52 -0500
 From: rgb r...@ellerbach.com
 Subject: Re: [Jmol-users] what is Jmol for?
 To: jmol-users@lists.sourceforge.net
 Message-ID: 4b2960c8.4060...@ellerbach.com
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 It detracts from the time devoted to the development of Jmol more than
 anything else. I don't disagree that some things might be of interest
 down the road but given the limited development resources I think they
 should be focused on the functionality related to the display of small
 and large molecules and the user interface of that use. If others from
 Sage or another environment want to build on Jmol's display capability
 then that is great and could be encouraged. Jmol is pretty modular and
 incorporating new functionality in some optional modules shouldn't  
 be a
 problem.

 Rich

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] first peak at update to Jmol in SAGE (3-D function plotting)...

[Jonathan Gutow]

Dear Jmol Users,
I'm trying to help the SAGEmath community update their usage of Jmol  
for viewing 3-D plots.  The link below will take you to a published  
sample on my local server.  I also use this for classes so it is a  
secure server with a self-signed certificate.  This  means you will  
get lots of warnings about possible security problems, just accept  
them to get a look.  Being a secure server and running on an old  
resurrected machine it may respond a little slowly at initial load, so  
please be patient.

I'd really appreciate comments from the Jmol community on what  
things might be nice to put in the web interface.

LINK: https://141.233.197.45:4443/home/pub/0

Thanks,
Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] first peak at update to Jmol in SAGE (3-D function plotting)...

[Jonathan Gutow]

Bob,
I would like to use some of these things, but first I am trying to  
understand how to get things to work inside of their server.  I've had  
to work around some issues with asynchronous updates coming from the  
server.  The other issue is that significant SAGE code will have to be  
rewritten to take advantage of this.  I'm trying to provide a smooth  
upgrade path that won't break worksheets produced in older versions of  
SAGE.  At present SAGE ships with 11.6.  I'm trying to migrate safely  
to 11.8 and when we release 11.10 so that there is a stable set of  
features, I will urge them to switch to that.  Now that I've dealt  
with some of their initial problems, I can also get a better list of  
what needs to be done.  What I think we want to do is define a plot  
primitive and have that generated in SAGE, rather than having them  
produce .pmesh (as they do now) or .jvxl as we've talked about some.
On Dec 15, 2009, at 5:51 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Tue, 15 Dec 2009 17:51:06 -0600
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] first peak at update to Jmol in SAGE (3-D
   functionplotting)...
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   ba9c0bd60912151551p22f1c7c1lae292641b42cb...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Jonathan,

 Here's an easy improvement -- use antialiasdisplay. It looks REALLY  
 nice
 with those graphs.
Good idea.  Hadn't thought of that.  What about the z-shade stuff  
(11.9 right?:().

 Say, is that a custom menu?
Yes, it is the custom menu that was generated for the SAGE notebook a  
while ago.  I haven't modified it, although I think it should be made  
to match the web interface features.  I'm waiting for feedback on what  
they want.

 One of the reasons that they might want to use Jmol 11.9.12 is that it
 includes the capability of drawing the intersection of an isosurface  
 with a
 plane. That means that they could be drawing lines on the surface that
 correspond with x, y, and/or z values. For example,

 isosurface iso1 PMESH x.pmesh 

 (isosurface and pmesh were merged in Jmol 11.7.12)

 then

 draw line1 width 0.1 intersection $iso1 x=1
 draw line2 width 0.1 intersection $iso1 x=2
 draw line3 width 0.1 intersection $iso1 x=3

 etc.

 would draw the expected contour lines. A set of these in two  
 directions
 would produce a standard grid-like mapping onto the pmesh. These  
 lines,
 because they are draw objects, could be sized and colored  
 appropriately and
 look very classy.



 Bob

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] first peak at update to Jmol in SAGE (3-D function plotting)...

[Jonathan Gutow]

Most of the issues relate to the user interface I'm trying to  
generate.  For example, to have clean control of the axes they've  
drawn from the user interface draw items need to have labels.  Sage  
Worksheets created so far don't name draw items in scripts, so I have  
to make some assumptions.  Another example is that as we fix bugs or  
enhance things they don't work exactly as they once did.  I already  
pointed out that there was an issue with the angle of frontlit between  
11.6 and 11.8, which is obvious when playing with simple SAGE  
surfaces.  I've worked around that in my code by issuing a pmesh o*  
fullylit command.  But this depends on the fact that presently SAGE  
names all the surfaces obj_XXX.  Anyway, I expect issues like this  
to continue.  I also find it very hard to build a web interface based  
on a moving set of features, so I'm playing with the 11.9 features,  
but expect the next version of Jmol in SAGE to be 11.8 (I hope very  
soon) and want to be ready to put 11.10 in when it comes out.  I'd  
like to see that include a plot primitive.

Since Jason is lurking here too maybe he can add to the following list  
of what it might contain.  My preliminary thoughts are a structure  
that contains:

1) An arbitrary number of isosurfaces, with attributes color,  
transparency, visibility, mesh color, mesh visibility, lighting state  
(fullylit default).  The range for the numbers in these isosurfaces  
should be limited only by the number range available for floating point.
2) Strings to title the X, Y and Z axes
3) Based on the range of the isosurfaces (pmeshes) provided Jmol would  
determine the bounding box and the scale adjustment for display.
4) This structure would have scriptable functions for turning on and  
off each of the edges of the bounding box, the axis titles and  
automatically computed numerical ranges on the axes (a real bonus  
would be if the tick numbers could be associated with any of four  
equivalent axes).  I think the SAGE solution of a minimum of 3 numbers  
per axis is pretty good.  Really big displays ( 600 px square) could  
benefit from 5 numbers per axis.

So ideally SAGE can just generate an unscaled list of isosurfaces,  
planes, etc.. Then Jmol would worry about making the plot pretty.

I think that the arbitrary intersections of planes and surfaces should  
continue to be accessed using the script methods already defined.

Part of the problem for me when dealing with lots of new features is  
that I don't have a whole lot of time to work on this.  I do it in  
five minute bits and pieces or for a while before bed instead of a  
crossword puzzle or reading a book

Jonathan

P.S. Did all the fixes related to an applet label of '0' get into  
Jmol.js?


On Dec 15, 2009, at 8:39 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Date: Tue, 15 Dec 2009 20:39:02 -0600
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] first peak at update to Jmol in SAGE (3-D
   functionplotting)...
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   ba9c0bd60912151839u21c1d2acr22cda3aa1a9c7...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Why would there be any compatibility issue, Jonathan? There should  
 not be
 any. Please let me know of any you are aware of.

 Bob

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] [Jmol-developers] isosurface plane error with non-orthogonal cell

[Jonathan Gutow]

I think you want to look at the contour functions.  See the jmol  
script documentation.  You need to describe better what you want to do.

Slab controls how far forward and backward in the view window stuff is  
drawn.

This is really a question for the users list.  I have redirected this  
discussion there.

Jonathan
On Dec 10, 2009, at 4:16 AM, Jan Brndiar wrote:

 Hi
  I'm using jmol to visualize some cross section throught the  
 isosurface
 but the cross section looks very strange

  load DENSITY.cube
  slab plane {0,0,1,-11}
  slab on
  isosurface p1 plane {0,0,1,-10} file 


 It's stratched and cutted... , but on the other side the isosurface

  isosurface s1 0.2 color red file  translucent

 looks good up to rotation which doesn't matter. I'm using the latest
 version of jmol 11.9.10. Older versions produce the same result.

 DENSITY.cube is located on http://147.213.112.235:/fotky/jmol/ 
 DENSITY.cube

 this is copy of the console output. I think it's a bug when drawing or
 creating cross section or it can be solved without crackdown to the  
 code.

 Jan Brndiar

 FileManager.getAtomSetCollectionFromFile(DENSITY.cube)
 FileManager opening /home/bxm/cpmd/jmol1/DENSITY.cube
 The Resolver thinks Cube
 openFile(DENSITY.cube): 115 ms
 ModelSet: haveSymmetry:false haveUnitcells:false  
 haveFractionalCoord:false
 1 model in this collection. Use getProperty modelInfo or getProperty
 auxiliaryInfo to inspect them.
 ModelSet: autobonding; use  autobond=false  to not generate bonds
 automatically
 isosurface p1 plane {0,0,1,-10} file ;
 FileManager opening /home/bxm/cpmd/jmol1/DENSITY.cube
 reading isosurface data from /home/bxm/cpmd/jmol1/DENSITY.cube
 data file type was determined to be Cube
 DENSITY: cube file created from cpmd Wannier file: DENSITY
  Total SCF Density

 voxel grid origin:(0.0, 0.0, 0.0)
 voxel grid count/vector:50 0.5619729 0.0 0.0
 voxel grid count/vector:50 0.28098598 0.48580202 0.0
 voxel grid count/vector:100 0.0 0.0 0.56691796
 JVXL read: 50 x 50 x 100 data points
 generateContours: 9 segments
 planar axes type 2 axis angle = 59.95507951548094 normal=(0.0, 0.0,
 0.86563313)
 planar vectors / lengths:(0.29738325, 0.0, 0.0) / 0.29738325
 planar vectors / lengths:(0.14869137, 0.25707534, 0.0) / 0.29697955
 unit orthogonal plane vectors:(1.0, 0.0, 0.0)
 unit orthogonal plane vectors:(0.50067884, 0.86563313, 0.0)
 unit orthogonal plane vectors:(0.0, 0.0, 0.86563313)
 nSquares = 2401
 generateContourData min=0.021693513 max=0.28818858 nContours=9 (0
 specified) contourFromZero=true
 generateContours: 6117 vertices
 ColorManager: color scheme now roygb color value range: 0.0 to 0.0
 color roygb range 0.021693513 0.28818858
 p1 created with cutoff = 0.0 ; number of isosurfaces = 1
 isosurface s1 0.2 color red file  translucent;
 FileManager opening /home/bxm/cpmd/jmol1/DENSITY.cube
 reading isosurface data from /home/bxm/cpmd/jmol1/DENSITY.cube
 data file type was determined to be Cube
 DENSITY: cube file created from cpmd Wannier file: DENSITY
  Total SCF Density

 voxel grid origin:(0.0, 0.0, 0.0)
 voxel grid count/vector:50 0.5619729 0.0 0.0
 voxel grid count/vector:50 0.28098598 0.48580202 0.0
 voxel grid count/vector:100 0.0 0.0 0.56691796
 JVXL read: 50 x 50 x 100 data points
 s1 created with cutoff = 0.2 ; number of isosurfaces = 2

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800 Algoma Boulevard FAX:920-424-2042
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  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Jmol displays NBOs in GAMESS and Gaussian

[Jonathan Gutow]

Xavier,
I'm not sure we have a way to get at all those things  
simultaneously.  The Mulliken (by default or Lowdin by request)  
partial charges are loaded into Jmol from GAMESS files.  I think the  
reader is pretty much exclusive for the NBO stuff, from what I  
remember (Bob?).  I haven't worked on this since Spring and will have  
to look back at the code.  I think things could be modified to allow  
what you want, but we may have things set up so that it won't work at  
present.

Jonathan
On Oct 27, 2009, at 6:39 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Message: 1
 Date: Tue, 27 Oct 2009 18:38:58 -0500
 From: Xavier Prat-Resina xav...@chem.wisc.edu
 Subject: Re: [Jmol-users] Jmol displays NBOs in GAMESS and Gaussian
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   980505e20910271638idefed64pb1f9ec272bd34...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Thanks for the fast response Bob.

 I meant to have access to the NBO charges at the same time as the  
 regular
 MOs,
 not the Natural Bond Orbitals.
 I'm using the same Gaussian file that contains a lot of information to
 display
 MOs, MEPs...etc and I prefer NBO charges rather than Mulliken.

 If I FILTER NBOCharges NBO I lose the MOs and the NBO charges are  
 in frame
 2 of
 the Gaussian file (in frame 1 charges are 0).
 On the other hand if I try something like FILTER NBOCharges !NBO
 I can display the MOs on frame 2 but I lose the NBOCharges and only  
 Mulliken
 seem to be available.

 I've been testing this in the same h2so4_nbo.log file that it's  
 available in
 the repository.
 http://xpr.chemeddl.org/~xavier/nbo/test2.htmlhttp://xpr.chemeddl.org/%7Exavier/nbo/test2.html
  
 
 Thanks for the help!!

 Xavier

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Remove Jmol Watermark

[Jonathan Gutow]

I agree that the Frank is not an obvious menu.  However, I don't think  
we should change the interface more than necessary. I suggest leaving  
the Frank where it is, with a translucent rectangular background  
containing a little triangle in a circle to the right of the Jmol.   
The background will  make it look something like a button/menu bar and  
the circle with a triangle is getting to be a pretty common indicator  
that you will get a pop-up or pull-down menu.

Jonathan
On Oct 19, 2009, at 2:18 PM, Jeff Hansen jhan...@depauw.edut wrote:

 Message: 4
 Date: Mon, 19 Oct 2009 15:18:14 -0400
 From: Jeff Hansen jhan...@depauw.edu
 Subject: Re: [Jmol-users] Remove Jmol Watermark
 To: jmol-users@lists.sourceforge.net
 Message-ID: b505957e-c778-46ae-8087-4dcd42e4a...@depauw.edu
 Content-Type: text/plain; charset=us-ascii

 David,

 You make a good point.  I don't remember having looked at your
 suggestion.  Here is another possibility.  Just having the word Jmol
 at the bottom right doesn't clue people in to the fact that it is a
 menu, as you said.  Putting at the top left and putting a bar across
 the top - just a slightly different color or lighter shade - would
 lead people to think it was a menu, which it is.


 Jeff

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Are others experiencing very broken javascript and Jmol pages in IE8?

[Jonathan Gutow]

Angel,
Thanks for the offer.  I've found the problem for web pages off of  
servers.  It appears that (as is often the case in MS products) you  
have to turn things on (and off) in more than one place to get them to  
work.  In IE 8 just choosing to allow active content when warned (ie  
Javascript and ActiveX) does not work.  You also have to go to Tools   
Internet Options  Security Tab  Custom Level... button and then make  
sure that Active Scripting and Scripting of Applets is enabled.  I  
would guess many people will not be able to get pages with applets and  
javascript working in IE8.

I haven't found how to get it to behave for local files.

Two comments:
1) IE8 appears to be 4 - 10 times slower than Firefox.
2) IE8 appears to have a nice developer's tools for debugging.   
However, on my test machine it is so slow, that I don't think I will  
have the patience to use it.

Jonathan
On Oct 4, 2009, at 7:27 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 From: Angel Herr?ez angel.herr...@uah.es
 Subject: Re: [Jmol-users] Are others experiencing very broken
   javascript and  Jmol pages in IE8?
 To: jmol-users@lists.sourceforge.net
 Message-ID: 4ac873c3.29219.d863...@angel.herraez.uah.es
 Content-Type: text/plain; charset=US-ASCII

 Dear Jonathan

 I haven't seen any major problems like you describe -- but I don't  
 test IE often.
 I've had XPsp3 for a long time now,so I would not suspect that.
 IE8 is another business, it seems to handle things a bit different,  
 has a better support for
 DOM/CSS standards, and particularly it has a new, better (well, at  
 least it's something) error
 report for javascript, so things that didn't show up in IE7 may now  
 be made prominent.

 If you can point out to some of your problem pages, I may test them  
 in my system.

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] Are others experiencing very broken javascript and Jmol pages in IE8?

[Jonathan Gutow]

hmm...is there some way I could have had things default to restrictive  
settings during my upgrade?

All I did was
1) upgrade my windows test machine to SP3
2) test pages in IE7 (most with javascript stopped working even when I  
allowed scripts to run at the warning)
3) thought maybe SP3 didn't play nice with IE7 so upgraded to IE8  
(same result)
4) things finally worked when I went in and manually set the active  
scripting and script applets to allowed in the tools internet  
settings custom level... dialog.

I found comments about this on the internet, so maybe we do need to  
somehow trap this (how? since javascript is completely shut down) and  
give people instructions on how to make it work.

See for example:
http://en.kioskea.net/forum/affich-118786-enable-javascript-in-internet-explorer-8

Once I got things working the only problem I've encountered is that  
IE8 does not implement node.parentNode.  I don't think we use that in  
Jmol.js, but I was using it to dynamically build a test page.

Jonathan
On Oct 4, 2009, at 7:52 PM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 Subject: Re: [Jmol-users] Are others experiencing very broken
   javascript and  Jmol pages in IE8?
 To: jmol-users@lists.sourceforge.net
 Message-ID:
   be3b9a200910041752i33996a98s908d270bd8ec2...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 I haven't noticed any severe problems with the testing I've done  
 (WinXP SP3,
 IE7 and IE8).  But I spend most of my time with Firefox.

 Dean

 On Sun, Oct 4, 2009 at 7:54 PM, Robert Hanson hans...@stolaf.edu  
 wrote:

 In case it's any consolation -- Windows 7 running MSIE 8.0.7100.0  
 works
 just fine. It's possible that one of my family members enabled  
 scripting for
 applets, but I doubt it. It's a recent build. Do we need to trap  
 this in
 jmolScript()?

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Are others experiencing very broken javascript and Jmol pages in IE8?

[Jonathan Gutow]

Dear Jmol users:
I was testing something I wrote to help out the SAGE  
(www.sagemath.org) developers who were running into memory constraints  
for Jmol applets  (they open too many on a page).  Anyway, my new code  
and my older pages work fine in FireFox on Windows, but I cannot get  
reasonable behavior (many just crash with cryptic page error  
messages) in IE 78 on Windows XP SP3 (I think things were working  
before SP3, but I'm not sure when things started to go south).
Has anybody else seen this and do we know what is going on?  I'm  
getting really tired of making special allowances for Microsoft's  
inability to meet the standards everybody else does.

Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Is anybody planning to present anything Jmol related at the Spring ACS meeting?...

[Jonathan Gutow]

Dear All:
I will be going to the Spring ACS meeting for reasons unrelated to  
Jmol.  However, if we don't have any (or many) presentations planned  
related to Jmol, I will submit an abstract to talk about it.  Probably  
to the Computers in Chemical Education symposium.  Please either  
encourage me or let me know that you are already planning to present.   
The deadline for abstracts is approaching fast.

Thanks,
Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] When using multiple Jmols in a window can you unload one of them?

[Jonathan Gutow]

Has anybody figured out how to unload a Jmol applet from a window  
and replace it with a picture?

I was asked this question on the SAGE (www.sagemath.org, open source  
mathematics/algebra system) discussion lists.  Some people are running  
in to memory constraints when they have lots of Jmol plots in the same  
web worksheet.  So the idea is to keep only one or two active applets  
in a page at a time.

Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-users] When using multiple Jmols in a window can you unload one of them?

[Jonathan Gutow]

I have my own answer.  The question is does this really free up the  
memory space used by the applet.

My solution is to use document.write in javascript to replace the  
contents of the div containing Jmol with a picture in place of the  
applet.

Anybody investigated this?

Jonathan

Begin forwarded message:

 From: Jonathan Gutow gu...@uwosh.edu
 Date: September 26, 2009 7:27:53 AM CDT
 To: jmol-users@lists.sourceforge.net
 Subject: When using multiple Jmols in a window can you unload one  
 of them?

 Has anybody figured out how to unload a Jmol applet from a window  
 and replace it with a picture?

 I was asked this question on the SAGE (www.sagemath.org, open source  
 mathematics/algebra system) discussion lists.  Some people are  
 running in to memory constraints when they have lots of Jmol plots  
 in the same web worksheet.  So the idea is to keep only one or two  
 active applets in a page at a time.

 Jonathan
 Dr. Jonathan H. Gutow
 Chemistry Department gu...@uwosh.edu
 UW-Oshkosh   Office: 
 920-424-1326
 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-users] Did your Jmol question get answered?

[Jonathan Gutow]

Alejandro,
Did your Jmol question get answered?  I use Jmol as an application  
all the time on MacOSX.  To do that just download the zip file from  
sourceforge, unzip and double click on the file Jmol.jar in the  
directory that is produced.  This directory can be stored anywhere on  
your computer.
If you are having trouble with Jmol in web sites I will need more  
information, such as the browser and the site you are having trouble  
with.

regards,
Jonathan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/faculty_staff/gutow/





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[Jmol-users] Could you generate some GAMESS-UK output files for us to check Jmol with?...

[Jonathan Gutow]

Dear Users:
Bob Hanson and I are working on fixing up the file readers for the  
GAMESS text output files (.gam, .out, .log).  I have a recent version  
of GAMESS-US running, but we need some files from GAMESS-UK to make  
sure we deal with the differences properly.  If you have access to  
GAMESS-UK and are willing to run a few small molecules for us (O2,  
HCl and some things like that), please contact me.  I'll send you my  
input files, so that we will be comparing the same calculations for  
the two versions.

Thanks,
Jonathan

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/faculty_staff/gutow/





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Re: [Jmol-users] Jmol and xhtml

[Jonathan Gutow]

I believe this is simply due to the fact that MSIE doesn't recognize  
the .xhtml extension.  My recollection is that .xhtml pages work if  
you use the .html extension and the proper xhtml header information.   
That said, I also recall that MSIE displays the pages formatted  
differently than the other browsers.  Anyway, try changing the  
extension before putting the page on a server.

These are the reasons why I didn't use .xhtml pages in the export to  
web function.

Jonathan
On May 7, 2009, at 7:05 AM, jmol-users-requ...@lists.sourceforge.net  
wrote:

 BTW, is anyone able to see xhtml pages in IE? My IE8 triggers a
 download --either asks or goes directly to be rendered in my default
 browser, Firefox.

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/faculty_staff/gutow/





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