Re: [Jmol-users] installing JSmol extension

[Jaime Prilusky]

Yes. And the surface looks great.

Note: if you want to avoid the simplified rendering of the surface while 
rotating the model, you may add 8 to the  block.

This sets platformSpeed as defined at 
https://chemapps.stolaf.edu/jmol/docs/#set_platformspeed

Jaim

> On 25 Jul 2017, at 20:23, Angel Herráez  wrote:
> 
> I've just visited (first time)
> http://dipc.ehu.es/bondslam/index.php/Hypervalence
> 
> and I can see both molecule and  surface
> 
> So either you just fixed it or there is some caching problem
> 
> 
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Re: [Jmol-users] installing JSmol extension

[Jaime Prilusky]

Dear Angel,
Please see below what I wrote Henry. Somehow JSmol sometimes fails reading the 
JVXL file.

From the existing files in jsmol/j2s/J/jvxl/readers/, I guess that the software 
finds out the format of the file to read, and call the matching reader. i.e 
PolygonFileReader.js for PoligonFile files, KinemageReader.js for Kinemage 
files, etc.

In this case it fails in detecting the file format for your JVXL file, produces 
UNKNOWN and fails again in loading UNKNOWNReader.js

On 25 Jul 2017, at 12:00 PM, Angel Herráez 
> wrote:

Hi Henry!


To me it sounds like some js library incompatibility (edit mode vs. view mode). 
The UNKNOWNReader part sound very suspicious.

What happens if, from the non-working page, you open JSmol console and paste 
the command to load the isosurface?


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[Jmol-users] JSmol labels on zoom

[Jaime Prilusky]

There’s not a proportional change of size of Labels when zooming a model on 
JSmol 14.9.1 (and maybe on other versions), both on zooming initiated by script 
and by interactive mouse driven. Labels remain with the original font size 
despite the change in size of the model.

Is there a way to control this?

Thank you,
Jaim
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Re: [Jmol-users] Fwd: SourceForge Project of the Week March 27th, 2017

[Jaime Prilusky]

Congratulations!!

On 23 Mar 2017, at 16:22, Robert Hanson 
> wrote:

FYI

-- Forwarded message --
Subject: SourceForge Project of the Week March 27th, 2017

Hi,

If you’re receiving this email it is because you are listed as an admin on our 
next Projects of the Week Issue for March 27th, 2017 on the SourceForge Blog.

Here are the projects selected:

otter-browser
cyberfoxportabl
pinn
jedit
jmol
skychart
dispcalgui
emmabuntus
d3.js

You will see them reflected live on the SourceForge homepage and blog next week.

Thanks,

Joan Nadene
SourceForge Community Coordinator



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Re: [Jmol-users] Jsmol mutate behaviour

[Jaime Prilusky]

Angel suggested yesterday the minimizing solution which works.

Thank you both!

Jaim

Here’s Angel complete solution:


mutate 148 SER;

select [SER]148:A;

color CPK;

wireframe 0.2;

color opaque;

minimize (selected and sidechain);

// alternative:  minimize fix (not (selected and sidechain));

delete selected and _H;

connect single modify;


On 1 Feb 2017, at 05:41, Robert Hanson 
> wrote:

(sorry for the delay -- the images were over the byte limit  for the list)

I just meant that I think the flexible fit algorithm in Jmol just uses the 
carbon atoms, not the rest of the atoms, so it is quite possible that a C-O 
bond will be rotated. Did you try minimizing?

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Re: [Jmol-users] Jsmol mutate behaviour

[Jaime Prilusky]

On 29 Jan 2017, at 2:39 PM, Robert Hanson 
> wrote:

Might be just the carbon atoms.

Can you please be more explicit?
What I’m doing wrong?
Is there a way to apply the mutate command and get the correct rendering?

[cid:858B8B02-0D68-4323-84FC-E861DF60A73B@weizmann.ac.il]


Please see the attached image. The same structure 5ELA , after applying the 
commands as follows:

On the left:
  select [SER]148:A;
  color CPK;
  wireframe 0.2;
  color opaque;

On the right:
  mutate 148 SER;
  select [SER]148:A;
  color CPK;
  wireframe 0.2;
  color opaque;

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[Jmol-users] Jsmol mutate behaviour

[Jaime Prilusky]

Something funny on the results I get from the mutate command.

By mutating a residue into the same residue, I was expecting no conformational 
change.

What I’m doing wrong? Same results with jsmol_14.6.1_2016.08.11 and 
jsmol_14.7.5_2016.12.02

Please see the attached image. The same structure 5ELA , after applying the 
commands as follows:

On the left:
  select [SER]148:A;
  color CPK;
  wireframe 0.2;
  color opaque;

On the right:
  mutate 148 SER;
  select [SER]148:A;
  color CPK;
  wireframe 0.2;
  color opaque;

[cid:2F923714-62B1-4AA9-A2C7-5F7C3D6A386C@weizmann.ac.il]
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Re: [Jmol-users] "Augmented Reality": https://github.com/es605/HTMoLar

[Jaime Prilusky]

I would say that Molecular Playground http://molecularplayground.org/ 
http://proteopedia.org/w/Molecular_Playground qualifies for an effective 'Use 
of Jmol on augmented reality'.

Jaim

On 15 Aug 2016, at 18:58, Angel Herráez 
> wrote:

I have had a little practice using Augmented Reality using a downloadable piece 
of software --by Colin Berry-- and molecular models exported (VRML) from Jmol:
http://www.cf.ac.uk/biosi/staffinfo/berry/AR/ar.html
doi:10.1002/bmb.20805

You need to run the software in the computer you want to use (Win / Mac), and 
do a little text editing on the config files. The models look very crisp; 
rotation is limited by its visibility of the marker card from the camera.
Spacefill, ball and stick, cartoons, molecular surface work fine.

Apart from being fashionable, I do not expect that any such viewer will match 
what can be done with JSmol embedded in a page.

https://github.com/es605/HTMoLAR
I don't quite see what's the role of AR there. You can see the structure within 
the web page before accessing the AR page where your webcam is activated and, I 
guess, for this to work you need to have printed the card with the 
symbol-marker-QR for the model you choose.

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Re: [Jmol-users] Capture PNGJ file as a variable

[Jaime Prilusky]

This should be the same as using preloaded images with javascript.
Jaim

> On 15 Jul 2016, at 11:51 AM, Angel Herráez  wrote:
> 
> El 14 Jul 2016 a las 12:13, Robert Hanson escribió:
>> Note that by putting a PNGJ file into a variable you can
>> 
>> -- extract or exchange the image
> 
> So a question would be, 
> How to apply that extracted image in the page, e.g. as the source of an 
>  tag created dynamically in Javascript?
> 
> 
> 
> 
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Re: [Jmol-users] incomplete cartoons in Calpha-only files

[Jaime Prilusky]

Jmol is unable to extract and render Sheet information from the new PDBe 
generated cif files, with chain IDs in sheet records are specified as A-2, A-3 
, see http://www.ebi.ac.uk/pdbe/coordinates/1stp/assembly?id=1



On 8 Jul 2016, at 5:09 PM, Herráez Sánchez Ángel 
> wrote:

Thank you, Bob

> I recommend that Proteopedia not remove the helix/sheet records.

Of course. That is feasible with the pdb files that were formerly used, and we 
had thought of it (me and Jaime).

The problem now is that Protepedia is now swiatching to using a copy of the 
"assembly" mmCIF file from PDBe, and for those files they seem to be using a 
different set of records / fields / format than for regular mmCIF files. That 
is making diagnosis more difficult. There might be a need to revise the Jmol 
reader for these files, or an adjustment on the part of PDBe of which fields 
they are including. We are after that. Thank you for your feedback.



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[Jmol-users] Jmol 14.6.0_2016.06..22 Saved State

[Jaime Prilusky]

Differences found on saved state from Jmol version 14.6.0_2016.06.22

SelectionHalos OFF; is not longer present in _setSelectionState() .  Will this 
come back on a next release?

There’s a new set cartoonsfancy false;  (notice the plural) in addition to the 
previous set cartoonfancy false;.

set selectallmodels true; is not longer present in _setParameterState() . Will 
this come back on a next release?


On Jun 23, 2016, at 9:37 AM, Robert Hanson 
> wrote:

Jmol.___JmolVersion="14.6.0_2016.06.22"

bug fix: compare(a,b,"isomer") does not detect ENANTIOMER (broken in 14.5.5)
bug fix: missing error trap for unsettable property setting
bug fix: load models {0 0 1} ... fails in script compiler

Download Jmol-14.6.0_2016.06.22-binary.zip (65.9 MB) 


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Re: [Jmol-users] JmolData.jar jmol-14.6.0_2016.05.24

[Jaime Prilusky]

On 14 Jun 2016, at 3:45 AM, Robert Hanson 
> wrote:

I don't think capture should work from JmolData. Try Jmol.jar

Thank you,
Jaim
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[Jmol-users] JmolData.jar jmol-14.6.0_2016.05.24

[Jaime Prilusky]

Could it be that command ‘capture’ fails on JmolData.jar from 
jmol-14.6.0_2016.05.24 ?

After loading a model, ‘ capture “file.gif” Y 30 ’ generates a file with only 
GIF89a?? on it.
On the other side, ‘ write IMAGE 500 500 GIF “file.gif” ‘ works Ok.

Jaim
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Re: [Jmol-users] JmolApplet.jar

[Jaime Prilusky]

Agreed. 
Signed Java can become handy in the distribution.
Files not needed for a functional JSmol, like examples, scripts, etc, can be on 
a separated download.

Jaim

> On 18 May 2016, at 12:38 PM, Angel Herráez  wrote:
> 
> I certainly would prefer to have Java available in the distribution. For 
> large 
> proteins and complexes there is still a significant difference in performance.
> 
> Maybe the nonsigned variant can be dropped / separated into the other 
> download
> 
> On the other hand, I would vote for not having the extra files in the 
> distribution like examples, scripts, copy of jQuery etc
> Just leave what is needed for an operative JSmol, HTML5+Java
> 
> 
> 
> 
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[Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

[Jaime Prilusky]

It seems that JSmol gets unloaded when a page gets out of focus, by flipping 
between pages, on Safari Mac Version 9.0.3 (11601.4.4).

1. Open any page on Safari  Mac (tested on Version 9.0.3)

2. Now open a page with JSMol on it, i.e. http://proteopedia.org/w/1dnn

3. Go to the previous page: History->Back or click on the ’Show the previous 
page’ arrow 

4. Go to the JSmol page: History->Forward or click on the ‘Show the next page’ 
arrow

JSmol is not longer reponsive.

This doesn’t happen on Chrome or Firefox on Mac. Doesn’t happen either on 
Safari when a page loose focus by opening another window on the same browser.

Jaim

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Re: [Jmol-users] JmolVersion="14.4.1_2016.01.04"

[Jaime Prilusky]

Thank you!
This release fixes the problem with scenes depending on default values.
Jaim
__

On 5 Jan 2016, at 5:58 AM, Robert Hanson 
> wrote:

Download Jmol-14.4.1_2016.01.04-binary.zip (18.2 
MB)

bug fix: (JvxlReader) Jmol 12 mapped isosurface jvxl files do not show mapped 
color
bug fix: setting cartoons on for phosphorus-only polymers fails
bug fix: setting default label properties using select none; fails
bug fix: undocumented model-based draw [array of points] broken
 -- points only
 -- selects from visible frames (frame *, for example)
 -- load cyclohexane_movie.xyz; frame *; draw 
@{{C5}.split().sub({1,0,0})




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it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Re: [Jmol-users] JSmol defaults for label ?

[Jaime Prilusky]

Can you please implement defaults again?

Jaim

On 3 Jan 2016, at 3:33 PM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:

Yes, that's  something I changed. Darn. When does it happen?

On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky 
<jaime.prilu...@weizmann.ac.il<mailto:jaime.prilu...@weizmann.ac.il>> wrote:
Unless we set defaults for labels, we get the following JSmol error: 
this.colixes is null, when using Jmol 14.4.1 2015-12-23

Same script works fine with previous 14.3.5_2014.08.09

Something is not loading as expected?

Regards,
Jaim

TypeError: this.colixes is null try/catch path:
0 function (b,d)
 args[0]=TypeError: this.colixes is null
 args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.executeCommands(a,b)
 args[0]=false
 args[1]=true
2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
 args[0]=false
 args[1]=false
 args[2]=false
 args[3]=false
 args[4]=null
 args[5]=true
3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
 args[0]=String
 args[1]=script ./JournalJBSD1Cv2.spt
 args[2]=
 args[3]=false
 args[4]=true
4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
 args[0]=String
 args[1]=script ./JournalJBSD1Cv2.spt
 args[2]=
 args[3]=false
 args[4]=true
5 JS.ScriptQueueThread.runNextScript()
6 JS.ScriptQueueThread.run1(a)
 args[0]=0
7 J.thread.JmolThread.run()
8 start()
9 function ()

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mail: jaime.prilu...@weizmann.ac.il<mailto:jaime.prilu...@weizmann.ac.il>

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Re: [Jmol-users] JSmol defaults for label ?

[Jaime Prilusky]

See http://proteopedia.org/wiki/tests/tstscene.html
Click on [scene 2] to load the scene.
The same scene works Ok after setting some font and alignment attributes (find 
"enabling the following defaults” in the script)

On 3 Jan 2016, at 4:58 PM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:

Please give me a script I can test.

On Sun, Jan 3, 2016 at 9:57 AM, Jaime Prilusky 
<jaime.prilu...@weizmann.ac.il<mailto:jaime.prilu...@weizmann.ac.il>> wrote:
Can you please implement defaults again?

Jaim

On 3 Jan 2016, at 3:33 PM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:

Yes, that's  something I changed. Darn. When does it happen?

On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky 
<jaime.prilu...@weizmann.ac.il<mailto:jaime.prilu...@weizmann.ac.il>> wrote:
Unless we set defaults for labels, we get the following JSmol error: 
this.colixes is null, when using Jmol 14.4.1 2015-12-23

Same script works fine with previous 14.3.5_2014.08.09

Something is not loading as expected?

Regards,
Jaim

TypeError: this.colixes is null try/catch path:
0 function (b,d)
 args[0]=TypeError: this.colixes is null
 args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.executeCommands(a,b)
 args[0]=false
 args[1]=true
2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
 args[0]=false
 args[1]=false
 args[2]=false
 args[3]=false
 args[4]=null
 args[5]=true
3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
 args[0]=String
 args[1]=script ./JournalJBSD1Cv2.spt
 args[2]=
 args[3]=false
 args[4]=true
4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
 args[0]=String
 args[1]=script ./JournalJBSD1Cv2.spt
 args[2]=
 args[3]=false
 args[4]=true
5 JS.ScriptQueueThread.runNextScript()
6 JS.ScriptQueueThread.run1(a)
 args[0]=0
7 J.thread.JmolThread.run()
8 start()
9 function ()

__
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R Bioinformatics and Data Management

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Re: [Jmol-users] Jmol-14.4.1_2015.12.21

[Jaime Prilusky]

Please check the build. There’s inside jsmol.zip two folders, jsmol and jsmol2


On 22 Dec 2015, at 6:21 AM, Robert Hanson 
> wrote:

Jmol-14.4.1_2015.12.21-binary.zip

JmolVersion="14.4.1_2015.12.21"

bug fix: color [0xff] should not be case-sensitive -- [0Xff] should be 
OK
bug fix: set spin fps ... fails
bug fix: array handling for labels very inefficient
bug fix: y = javascript("x") only creates string equivalent of x, not actual 
numerical/object values
bug fix: y = javascript("x") draws "x" from wrapped anonymous function using 
eval() instead of global context using window.eval()

code: (JavaScript) adding use of typedArray.buffer.slice
code: (JavaScript) adding use of array.slice and implementing Java  byte[] as 
JavaScript Int8Array()


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Re: [Jmol-users] test please

[Jaime Prilusky]

Too many errors while converting pyMOL pse files.

See for example 
http://noys3.weizmann.ac.il/a2jb/browse?sn=testSet/1bna_surface/loadPSEfileERR.txt
or 
http://noys3.weizmann.ac.il/a2jb/browse?sn=testSet/2008_09_11_GOLD/loadPSEfileERR.txt

Note: Jmol.___JmolVersion=“14.4.1_2015.12.20"
__
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R Bioinformatics and Data Management

mail: jaime.prilu...@weizmann.ac.il<mailto:jaime.prilu...@weizmann.ac.il>
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)

On 21 Dec 2015, at 1:37 AM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:

I have made some significant changes to the way JSmol handles arrays. This 
needs wider testing -- Mac OS especially, JavaScript/HTML5 specifically.

The full code is at:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.0_2015.12.20.zip


But you could also just test it at

http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm

if you want to.

If something is wrong, it will be immediately obvious. Specific tests that will 
be helpful are from the middle column and include anything that is binary: the 
PyMOL session file, the water.xyz.gz, 1hxw.png, square_planar.spartan, among 
others.

Mostly what I did was to implement byte arrays (Int8Array in JavaScript) and 
much faster array manipulation using .slice().

Maybe also making images.

I think this may break Internet Explorer 9, but that might not be a big deal -- 
there were just 300 visits out of 250,000 from that. But also Maybe Safari 5.1 
will break. again, only very few visits from that. Maybe time to move on.


Bob

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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it is better to take what answer we get.

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Re: [Jmol-users] Jmol -- testing requested

[Jaime Prilusky]

Thank you.

This new version fixed the Errors on missing Isosurface file: 
electrostatics2, 3BSN_3BSO, hupa_LC, HupA_2 and HupA_3

The rest stays:

The error of PyMOL reader not reading H69 as helix 
(RGS-Ga_8pdb_structures_aligned_S90_20.5.15.pse) persists. The generated JPNGJ 
contains two frames, the first one appears black. This is not reported as a 
conversion time error and can be browsed at 
http://noys3.weizmann.ac.il/a2jb/browse?dsp=MUL

Java crash error: WD_1rpusessionforpymoltests

Errors related to CGO: CGOtext, bbPlane and 3cmq_design_results


On Aug 19, 2015, at 5:12 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

I do not understand why sometimes the  build Jmol.jar does not match what I 
have when debugging. But that was the culprit with Rolf's problem.

http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.08.19-binary.zip/download

Jmol.___JmolVersion=14.3.16_2015.08.19

bug fix: PyMOL reader does not load surface from PNGJ file
bug fix: PDB reader can skip assignments of secondary structure after first 
structure loaded during session
bug fix: bad build of Jmol.jar
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Re: [Jmol-users] Load multiple models

[Jaime Prilusky]

 frame all; will help

 On Jul 27, 2015, at 9:35 PM, Thomas Hrabe thr...@gmail.com wrote:
 
 Hi there,
 
 I have problems with loading multiple pdbs into one view:
 
 
 Jmol.script(applet,'load FILES 
 http://fatcat.burnham.org/fsn-data/chains.superimposed/1pzuB.1a02N.pdb; 
 http://fatcat.burnham.org/fsn-data/chains.superimposed/3qrfM.1a02N.pdb; 
 ;display *;’)
 
 The applet shows only the first model.
 
 Thanks,
 Thomas
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Re: [Jmol-users] Chemical elements and counts

[Jaime Prilusky]

 On Jul 15, 2015, at 11:46 PM, Robert Hanson hans...@stolaf.edu wrote:
 Most recent Jmol version allows
 X = Jmol.evaluateVar(jmolApplet0, {*}.element.pivot
 
 $ load =1crn
 $ print {*}.element.pivot
 {
   C  :  1017
   H  :  532
   N  :  268
   O  :  375
   S  :  10
  }

What exactly happens with the atoms when you load a structure?

By simply counting atoms in 1crn.xml.gz under PDBx:type_symbol, I get the 
values below, and no Hydrogen which I assume Jmol is adding by default.

'C' : 202,
'N' : 55,
'O' : 64,
'S' : 6

What I’m missing here?

Jaim
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[Jmol-users] Jmol 14.3.13_2015.05.19 viewer.getBoolean(navigateSurface)

[Jaime Prilusky]

Executing headless JmolData.jar (see below the command line executed) from Jmol 
14.3.13_2015.05.19 reports three times

viewer.getBoolean(navigateSurface) - not listed

while this message is not present on the same operation on older versions of 
Jmol, i.e.  14.1.8_dev_2014.01.23

/usr/bin/java -Djava.awt.headless=true -jar JmolData.jar -nRJ 'exit;’

Is this just a warning? Does this affect the operation of JmolData.jar ?

Jaim


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Re: [Jmol-users] Add hydrogens to PDBs after they are loaded

[Jaime Prilusky]

Brenton,

On the script you currently use, you should be able to add pdbAddHydrogens 
before loading, as here:

set pdbAddHydrogens true; load= 2ace; 

Regards,
Jaim

 On Apr 21, 2015, at 8:56 AM, Brenton Horne brentonho...@ymail.com wrote:
 
 Hi,
 
 I have been using the JSmol extension for MediaWiki and I'd like to know 
 what script argument I need in order for hydrogens to be added to a 
 fetched PDB file. But as I can't run commands for this extension before 
 the PDB is fetched (e.g., I'd use set pdbAddHydrogens TRUE if I could 
 run commands before the PDB was loaded) because I'm using jmolPdb tags 
 I'm left asking which commands I can run after fetching the PDB file 
 that will add hydrogens to the ligands and solvent.
 
 Thanks for your time,
 Brenton
 
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Re: [Jmol-users] MediaWiki Jmol Extension

[Jaime Prilusky]

The current version of JSmolExtension does support both HTML5/Javascript and 
Java.

Proteopedia detects and supports mobile clients, switching between Java and 
HTML5 based on the client available engine. Proteopedia also supports editing 
of Jmol scenes from iPad.

Some examples of the current version of JSmolExtension  available at 
http://proteopedia.org/w/User:Jaime_Prilusky/JSmolExtension

Installing the JSmolExtension on MediaWiki is straightforward. Download the 
extension either from  
http://proteopedia.org/wiki/support/JSmolExtension/JSmolExtension.zip or from 
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-extensions/ and follow 
the few steps from the readme.txt file.

Please let me know if you encounter any problem.

Jaim

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On Feb 6, 2015, at 8:48 AM, Jim Hu 
jim.hu.bio...@gmail.commailto:jim.hu.bio...@gmail.com wrote:

I think you might want to consider the JSmol extension from Proteopedia for 
MediaWiki, or some way to switch between Jmol and JSmol based on the client (I 
don't recall whether Proteopedia does that). One reason I've switched EcoliWiki 
to JSmol and developed the JSmol2wp Wordpress plugin is so that more users can 
see the applets even if they are on mobile or don't know how to deal with the 
Java security restrictions on other machines. If I was doing it for a user base 
like a class, where I had more control over the machines being used, I might 
prefer the Java based Jmol. But for a lot of web uses JSmol will reach a larger 
base of users, IMO.

Jim
On Feb 5, 2015, at 7:53 PM, Brenton Horne 
brentonho...@ymail.commailto:brentonho...@ymail.com wrote:

Hi, Nico

Yep that was me that asked about the extension on the talk page @ MW. Yeah, I 
saw that Angel  Bob were listed as editors/contributors in Sourceforge and 
other places hence why I thought they may be able to help me.

Brenton

On 6/02/2015 11:27 AM, Nicolas Vervelle wrote:
Hi Brenton,

Documentation on MediaWiki is probably completely outdated.
I was the one who wrote it originally, but it was a long time ago, and since 
modifications have been made to the extension and many versions of MW have been 
released.
Are you also the one who asked about this on the extension talk page in MW ?
https://www.mediawiki.org/wiki/Extension_talk:Jmol

I'm currently travelling until mid February, I can't do much until then.
Other people here will probably help you, since the extension is running on 
several wikis I believe.

Nico

On Thu, Feb 5, 2015 at 9:38 PM, Brenton Horne 
brentonho...@ymail.commailto:brentonho...@ymail.com wrote:
Hi,

I see many developers of Jmol also helped develop the MediaWiki Jmol
extension, hence why I felt this would be a decent enough place to ask
for help with it. I followed the installation instructions @ MediaWiki's
Extension:Jmol page, without any obvious problems.

Then when all the steps were finished (including checking
special:version to see if the extension was added, which it was) I
tested it out by adding jmolPdb3EIG/jmolPdb (and other Jmol-related
wikitext like jmolFile(S)-nicotine.sdf/jmolFile where
(S)-nicotine.sdf is the name of a file on my Wiki) to a random page and
clicking submit. This resulted in me being left at a blank submit page
(i.e., with PAGENAME?action=submit in the address bar). I have tried and
retried this just in case I encountered some random server problem, but
each time I got the same results.

I have since customized my Jmol.body.php file and the structure/naming
of the jsmol extension direct according to the file locations specified
in Jmol.body.php in an attempt to overcome this problem. I have had some
(sort of) success in that now I can save a page with these tags in it
without that submit error, but JSmol applet still isn't embedded into
the page. Rather where these tags are placed the PDB ID or file name
appears and is hyperlinked to a javascript command.

If it helps this is my current Jmol.body.php script:
https://drive.google.com/file/d/0B1_sXH68hMWBT1VrMTRNbzJSOHM/view?usp=sharing.

Thanks for your time,
Brenton

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Re: [Jmol-users] Safari reloading JSmol over and over

[Jaime Prilusky]

Had similar problems on Mac OS X 10.9.5 Safari 7.1 while testing FirstGlance 2.2

I would say that's the results of running JSmol with loaded portions from 
different versions. 

The problem disappeared after clearing cache and reseting Safari a couple of 
times.

Jaim

On Sep 30, 2014, at 1:37 AM, Robert Hanson hans...@stolaf.edu wrote:

 JUST saw that in a class of students here at St. Olaf using Otis's Virtual 
 Model Kit. 
 
 It was a Macbook Air with a new version of Safari released yesterday, I was 
 told. Certainly that must run far deeper than Jmol. Not much we can do about 
 that. 
 
 A bad week for Apple, perhaps. 
 
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Re: [Jmol-users] visible vs. restrict

[Jaime Prilusky]

On Sep 18, 2014, at 8:18 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.17.zip

bug fix: spin broken in WebGL (Jaime)

spin still broken on Mac, Safari, FFox and Chrome.

set antialiasDisplay ON/OFF also broken.

Menu-About-Jmol reports the correct latest version.

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Re: [Jmol-users] quality of the model

[Jaime Prilusky]

set antialiasDisplay ON

http://chemapps.stolaf.edu/jmol/docs/#setantialiasing

Jaim

On Sep 16, 2014, at 3:54 PM, GABRIEL PONS IRAZAZABAL 
gp...@ub.edumailto:gp...@ub.edu wrote:

My question is:
In first Glance Jmol, from Eric Martz, there is an option to improve the 
quality of the display. Could you tell me which is the sintaxis for this order 
in jmol console?

gabriel Pons

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Re: [Jmol-users] jmol-14.3.7_2014.09.07c

[Jaime Prilusky]

Great!. Now the version appears correct.
Mouse interacts with WebGL rendering.
spin on applet while on WebGL appears broken.
More testing later.
Jaim

On Sep 8, 2014, at 3:56 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

Oy, that explains A LOT. Looks like since mid August the zip files at St. Olaf 
have had updated Jmol.jar versions but not JSmol.zip. My goodness. OK. Make 
that:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.08.zip

On Sun, Sep 7, 2014 at 10:52 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
On the file I downloaded, the file j2s/Jmol.properties reports old version:

___JmolDate=$Date: 2014-08-14 15:07:40 -0500 (Thu, 14 Aug 2014) $
___fullJmolProperties=src/org/jmol/viewer/Jmol.properties
___JmolVersion=14.3.6_2014.08.14

On WebGL Mac Firefox and Safari: spin is not working and mouse interaction 
broken.

Other basic functionality seems Ok both with Jmol.isAsync true and false.

Jaim

On Sep 8, 2014, at 5:38 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.07c.zip

Fixes some recently described bugs but also tries some new ways to load files, 
so no guarantees! I would appreciate testing, especially on Macs and tablets, 
which I have not done myself. I have tested it on Firefox, MSIE, and Chrome for 
Windows.

What I am experimenting with is fully asynchronous file transfer, both for data 
files and for code files. I have made a lot of progress, but it is still not 
ready. The setting

 Jmol._isAsync

set to true would enable that, but it is set to false. What I need to know is, 
with it set false, which is supposed to be essentially what we have had before, 
does everything work? There was a lot of adjusting in the code, so probably not.

If you want to experiment with

Jmol._isAsync = true

feel free. I know that is only partially working. Some classes still don't load 
asynchronously. And some that do don't report back properly when they are 
loaded in order to resume processing correctly. I can load caffeine and PDB 
files and XML files. The console log looks MUCH cleaner, though:

JSmol load jmolApplet0 loadClazz... JSmol.min.js:268
JSmol load jmolApplet0 start applet... JSmol.min.js:268
JSmol exec jmolApplet0 loadClazz null -- OK JSmol.min.js:270
JSmol exec jmolApplet0 start applet null -- OK JSmol.min.js:270
xhr.open async=true url=data/caffeine.mol JSmol.min.js:177
syntax error caffeine.mol:1
xhr.open async=true url=http://www.rcsb.org/pdb/files/1d66.pdb; 
JSmol.min.js:177
xhr.open async=true url=http://www.rcsb.org/pdb/files/1d66.pdb; 
JSmol.min.js:177
xhr.open async=true url=http://www.rcsb.org/pdb/files/1blu.pdb; 
JSmol.min.js:177
xhr.open async=true url=http://www.rcsb.org/pdb/files/1d66.pdb; 
JSmol.min.js:177
xhr.open async=true url=http://www.rcsb.org/pdb/files/4tra.pdb; 
JSmol.min.js:177
xhr.open async=true url=data/estron.cml JSmol.min.js:177
xhr.open async=true url=data/vasp.xml JSmol.min.js:177
xhr.open binary async=true url=data/dna.pse JSmol.min.js:192

Note that there are no notifications for code .js files, because all of those 
are now coming in asynchronously as DOM script objects.

Specifically, note the missing message:

Synchronous XMLHttpRequest on the main thread is deprecated because of its 
detrimental effects to the end user's experience. For more help 
http://xhr.spec.whatwg.org/

because there is no synchronous file transfer for those cases. So that is 
definitely progress, and I am convinced it will all work soon enough.

Bob




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Re: [Jmol-users] The world of Jmol - an update: crystallography

[Jaime Prilusky]

Wow!! Thank you for the update and the glimpse into a busy present and a 
promising future.
(‘The world of Jmol’, nice title for an ongoing story)
Jaim

On Sep 4, 2014, at 2:53 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

[Sorry for the blog-like nature of this message. I'm not ready to blog yet -- 
maybe Henry Rzepa can take this on :) ]

I have just come back from the IUCr World Congress meeting in Montreal
conference: http://www.iucr2014.orghttp://www.iucr2014.org/
presentation: http://stolaf.edu/depts/chemistry/bh/iucr2014

and the SMARTER 4 conference in Durham UK
conference: http://www.ccpnc.ac.uk/smarter4
presentation: http://stolaf.edu/depts/chemistry/bh/durham2014

[Note that That is not meant to be self-explanatory, but the pictures are 
pretty!]

Now back to normal life after 15 months of sabbatical during which the main 
foci ended up being
  (a) database integration with Jmol and
  (b) crystallography,
I thought I would give a bit of update on (b). I won't cover everything here. 
Just get a discussion going.

XRD and XRPD

Jmol is thriving like never before. It has been embraced in all areas of 
chemistry, in materials science, in computational physics, and in 
crystallography (both single-crystal [XRD] and powder diffraction [XRPD]). We 
are really having a very broad impact on science!

XRPD, in particular, has made many advances recently, and is now providing full 
structure models, just like XRD. Estimates I heard were in the range of roughly 
100 new XRPD structures per year, and growing.

Jmol is the preferred viewer in this area because it can handle all aspects of 
CIF file structure definition.

3D EDT

If you do not know about the emergent field of Precession 3D Electron 
Diffraction Tomography http://www.edt3d.com/ [3D EDT], you might want to do 
some Googling. See, for example,

http://www.microscopy-analysis.com/magazine/issues/structure-determination-nanocrystals-precession-3d-electron-diffraction-tomography

Expect one or more Nobel prizes in this area. It is set to totally 
revolutionize crystallography.

The basic idea is that it is now possible to take a nanocrystal, place it in 
the vacuum of a standard scanning electron microsope, and record the 
diffraction of electrons from it at various beam angles. The phrase anyone can 
do it is not far off. The results can be integrated to get unit cell 
measurements in minutes and atomic resolution crystal structures after further 
analysis. Software is still under development, but it is likely that Jmol will 
be a significant part of that.

[3+n]D

Jmol is one of just a few software packages that can be used to visualize 
incommensurately modulated crystal structures, which can be understood using 
higher dimensional space groups (4D, 5D, thus  [3+n]D where n=1 or n=2). see 
http://infoscience.epfl.ch/record/183336/files/aperiodic_structures_infoscience.pdf

These are crystal structures that have unit cells, but each one is slightly 
different. It's really not so difficult to understand why that might be. A 
classic case is a misfit layer compound. See, for example, 
http://www.mdpi.com/1996-1944/3/4/2606.

These crystalline compounds have two or more semi-independent unit cells. Each 
unit cell is incommensurate with the other -- one or more of its dimensions 
is not a multiple or rational fraction of the other -- so they never line up, 
and since they are in the same physical crystal, the presence of one 
modulates the structure of the other.

There aren't a lot of these structures around, but their numbers are growing as 
crystallographers become more familiar with the new techniques and software 
tools that are being developed that can be used for structure solving and 
visualization.

The images you can create of these systems using Jmol are stunning and 
informative. I'm pretty sure there is absolutely nothing else like Jmol out 
there that can do this sort of thing. Expect Jmol integration into standard 
processing programs used in this area (such as Jana2006) soon.

I had better stop there for now

Bob

-

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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[Jmol-users] inactive mouse with WebGL

[Jaime Prilusky]

Can you please verify if mouse interaction is broken for WebGL? Tested Firefox 
and Safari on Mac 10.9.4

Applet renders structure Ok, but mouse can’t interact (rotate, zoom, open menu, 
etc).
Interaction from page works Ok (links, buttons, pulldown, etc). See either

http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?_USE=WEBGL ( version 
14.3.7_2014.08.22 )

http://wiki.jmol.org/index.php/Uploaded_XYZ_File?use=webgl  ( version 
14.2.4_2014.08.03 )

http://proteopedia.org/wiki/index.php/User:Jaime_Prilusky/JSmolExtension?use=webgl
 ( version 14.3.5_2014.08.09 )

Jaim
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Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

[Jaime Prilusky]

This seems to be a Chrome problem.
Try with Firefox or Safari before trying to fix your server.
Jaim

On Sep 3, 2014, at 12:33 PM, Mark Wass 
m.n.w...@kent.ac.ukmailto:m.n.w...@kent.ac.uk wrote:

Hi,

I am currently trying to get Jsmol to work on my server. I have used Jsmol 
successfully on other servers but this time I can’t get it to work. As a test I 
am simply trying to load a PDB file but when I try to load the page I get the 
following message:

Error connecting to server: 
http://www.sbg.bio.ic.ac.uk/3dligandsite/jmol-14.2.4_2014.08.03/jsmol/php/jsmol.php?call=getRawDataFromDatabasedatabase=_query=http%3A%2F%2Fwww.sbg.bio.ic.ac.uk%2F3dligandsite%2Fmodel.jmol.pdbencoding=base64

The page then displays the following:

Unrecognized file format for file
http://www.sbg.bio.ic.ac.uk/3dligandsite/model.jmol.pdb

!DOCTYPEE HTML PUBLIC “-//ETF//DTD HTML 2.0/EN”


htmlhead
title500 Internal Server Error/title


I have tried with different versions of Jmol without success. Any suggestions 
on how I can resolve this would be appreciated. I have copied the code fro mthe 
page below:

In the header I have the following code:

script type=text/javascript 
src=jmol-14.2.4_2014.08.03/jsmol/JSmol.min.js/script
script type=text/javascript 
src=jmol-14.2.4_2014.08.03/jsmol/js/Jmol2.js/script
script type=text/javascript
Jmol._alertNoBinary = false;
var jmolApplet0 = null;

var JSInfo = {
addSelectionOptions: false,
color: #00,
j2sPath: jmol-14.2.4_2014.08.03/jsmol/j2s,
// HTML5 only
use: HTML5,
width: 900,
height: 900,
disableJ2SLoadMonitor: false,
readyFunction: null,
deferApplet: false,
src: null,
serverURL: 
http://www.sbg.bio.ic.ac.uk/3dligandsite/jmol-14.2.4_2014.08.03/jsmol/php/jsmol.php;
}
/script

Then in the body I have:

script type=text/javascript
jmolApplet0 = Jmol.getApplet(jmolApplet0, JSInfo);
Jmol.script(jmolApplet0, load model.jmol.pdb;);
/script


Many thanks,
Mark

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Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

[Jaime Prilusky]

On Sep 3, 2014, at 12:49 PM, Mark Wass 
m.n.w...@kent.ac.ukmailto:m.n.w...@kent.ac.uk wrote:
Thanks for the suggestion Jaim.
It works properly in firefox but not in Safari.
Is there a fix to get it working in Chrome and Safari?

I’m also looking for  a solution :-)

I remember for this or a related problem being mentioned on this list some time 
ago.

Jaim
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Re: [Jmol-users] inactive mouse with WebGL

[Jaime Prilusky]

On Sep 3, 2014, at 3:37 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
Thanks -- I will check this before the next release. It is broken on chemapps, 
but it is not broken on my local site, suggesting that I just need to update 
the files on chemapps. Check 
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.08.29.zip please

Retrieved and expanded 14.3.7_2014.08.29.zip

Mouse still inactive when WebGL, despite clearing browser’s cache.

State on Console reports
# Jmol state version 14.3.6_2014.08.14  2014-08-14 15:07;
but this is also the info on jsmol/j2s/Jmol.properties

Jaim


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Re: [Jmol-users] support needed -- XHR -- asynchronous vs synchronous

[Jaime Prilusky]

Bob,

Can you please provide a template letter?

Jaim

On Aug 31, 2014, at 1:45 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

Folks, I would appreciate some letter-writing support in relation to

http://lists.w3.org/Archives/Public/public-webapps/2014JulSep/0084.html
http://lists.w3.org/Archives/Public/public-webapps/2014JulSep/0377.html

I don't know if you can respond directly to that list or not. I think you can. 
Please, if you do, be polite -- just share the importance of JSmol. Ask them to 
remove the recommendation to browser developers to experiment with breaking 
all our pages.

The executive summary is that if this recommendation is taken:

quote src=http://xhr.spec.whatwg.org/
Developers must not pass false for the async argument when the JavaScript 
global 
environmenthttp://www.whatwg.org/specs/web-apps/current-work/multipage/infrastructure.html#javascript-global-environment
 is a document 
environmenthttp://www.whatwg.org/specs/web-apps/current-work/multipage/webappapis.html#document-environment
 as it has detrimental effects to the end user's experience. User agents are 
strongly encouraged to warn about such usage in developer tools and may 
experiment with throwinghttp://dom.spec.whatwg.org/#concept-throw an 
InvalidAccessErrorhttp://dom.spec.whatwg.org/#invalidaccesserror exception 
when it occurs so the feature can eventually be removed from the platform.
/quote

All, and I mean ALL current JSmol implementations will stop working instantly.

I'm not sure the writers of that understand the implications for science and 
science education. Some word from others in prominent positions might help.

I would prefer they not just hear from me. Don't over-do it, just help them see 
what such experimentation would do to us.

That said, I am making good progress making FUTURE JSmol implementations 
totally asynchronous. I'm actually very close. I have a test version that loads 
everything asynchronously other than shapes, and it almost works. (Famous last 
words!)

But current pages using Jmol.getPropertyAsArray() or Jmol.evaluateVar() will 
absolutely be broken and will need some rewriting even if I do get a totally 
asynchronous version of JSmol running. Because those are inherently synchronous 
methods, and at least their first use requires an asynchronous  process.

I do have some ways around that. Basically you can effect (asynchronous) module 
loading in Jmol (the to-be asynchronous part) by issuing calls to 
Clazz._4Name(). For instance:

  Clazz._4Name(JV.PropertyManager)

just after applet creation will load the code that will later be used for 
Jmol.getPropertyAsArray() or Jmol.evaluateVar()

But obviously this will take updating of current web pages.

Bob


--
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Chair, Department of Chemistry
St. Olaf College
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http://www.stolaf.edu/people/hansonr


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it is better to take what answer we get.

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Re: [Jmol-users] jmol-14.3.7_2014.08.25.zip

[Jaime Prilusky]

JSmol.min.js reports TypeError: 'undefined' is not an object (evaluating 
'a._checkDeferred’) when sending scripts from a web page via JavaScript.

Entering same commands on the JSmol applet Console works Ok.

I assume that I’m testing the correct version. Expanding 
jmol-14.3.7_2014.08.25.zip, the file j2s/Jmol.properties reports an older 
version (14.3.6_2014.08.14), not 14.3.7_2014.08.25

Jaim

On Aug 26, 2014, at 6:31 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.08.25.zip

Just one minor fix, but what is perhaps interesting here is some low-level 
rewriting I did of a couple of core JavaScript implementations of Java classes 
(ArrayList, Hashtable) as well as the main j2sjmol.js library code that looks 
like it is speeding up some processes by up to 10-15%. The core methods in 
those important and much-used classes were somewhat inefficient.

___JmolVersion=14.3.7_2014.08.25

bug fix: translation of atoms after deleting atoms having dots on crashes Jmol

I hope to synchronize this with 14.2 later this week.

Bob

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Re: [Jmol-users] jmol-14.3.7_2014.08.25.zip

[Jaime Prilusky]

Dear Bob,

I’m downloading again and expanding  
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.08.25.zip
The file j2s/Jmol.properties states ___JmolVersion=“14.3.6_2014.08.14
How this can be a caching problem?

On Aug 26, 2014, at 3:17 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

That comes from

Jmol.script = function(applet, script) {
if (applet._checkDeferred(script))
return;
applet._script(script);
}


Which might imply someone forgot the applet parameter.



On Tue, Aug 26, 2014 at 7:14 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
I'm guessing that is a caching problem?


On Tue, Aug 26, 2014 at 2:24 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
JSmol.min.js reports TypeError: 'undefined' is not an object (evaluating 
'a._checkDeferred’) when sending scripts from a web page via JavaScript.

Entering same commands on the JSmol applet Console works Ok.

I assume that I’m testing the correct version. Expanding 
jmol-14.3.7_2014.08.25.zip, the file j2s/Jmol.properties reports an older 
version (14.3.6_2014.08.14), not 14.3.7_2014.08.25

Jaim

On Aug 26, 2014, at 6:31 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.08.25.zip

Just one minor fix, but what is perhaps interesting here is some low-level 
rewriting I did of a couple of core JavaScript implementations of Java classes 
(ArrayList, Hashtable) as well as the main j2sjmol.js library code that looks 
like it is speeding up some processes by up to 10-15%. The core methods in 
those important and much-used classes were somewhat inefficient.

___JmolVersion=14.3.7_2014.08.25

bug fix: translation of atoms after deleting atoms having dots on crashes Jmol

I hope to synchronize this with 14.2 later this week.

Bob

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Re: [Jmol-users] applet with multiple isosurfaces

[Jaime Prilusky]

Thank you.
Jaim

Sent from the grandson of my Apple ][

On 17/08/2014, at 21:42, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

show isosurface works on the currently selected isosurface. Selection is by 
issuing by itself:

isosurface ID x

Bob


On Sat, Aug 16, 2014 at 1:25 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
On Aug 16, 2014, at 9:24 PM, Angel Herráez 
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:
 There is isosurface list, which returns the IDs and some data, but not the
 jvxl data
 You are giving an ID to each surface, right?
 Otherwise only the last isosurface is accessed by most commands.

Yes. I do have an ID for each isosurface.

The command show isosurface I use to retrieve the JVXL data doesn't seem to 
accept an ID as argument. Tried different formats.




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St. Olaf College
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[Jmol-users] applet with multiple isosurfaces

[Jaime Prilusky]

After creating multiple isosurfaces, how do I get the list of the IDs defined 
isosurfaces and their data in JVXL format?

The following two commands seem to act on only one isosurface. They do return 
info and data of the latest isosurface defined

getProperty isosurfaceInfo
show isosurface

The data for all isosurfaces is there. The command isosurface cache lists all 
defined isosurfaces. I could parse this to get the IDs for the isosurfaces. How 
do I retrieve the JVXL data for each one?

Thank you in advance,
Jaim
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Re: [Jmol-users] applet with multiple isosurfaces

[Jaime Prilusky]

On Aug 16, 2014, at 9:24 PM, Angel Herráez angel.herr...@uah.es wrote:
 There is isosurface list, which returns the IDs and some data, but not the 
 jvxl data
 You are giving an ID to each surface, right?
 Otherwise only the last isosurface is accessed by most commands.

Yes. I do have an ID for each isosurface. 

The command show isosurface I use to retrieve the JVXL data doesn't seem to 
accept an ID as argument. Tried different formats.




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Re: [Jmol-users] Jmol select chains in large structures

[Jaime Prilusky]

Dear Bob,
Thank you for a prompt reply.
It does work when using the proper chain identifier.
Regards,
Jaim

On Aug 14, 2014, at 4:32 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

Unfortunately, the  chain designations used by Jmol to create the complete 
model,

_atom_site.label_asym_id

 are not the ones you refer to with chain=,

_atom_site.auth_asym_id

For example, in 1vu4 we have:

ATOM 68679 C CA  . VAL MA 1 36  ? 215.540 621.913  480.029 1.00 0.00 ? ? ? ? ? 
? 36  VAL m CA  1

MA is the label_asym_id; m is the auth_asym_id

This is just the way  it is. You need to use

 set chaincasesensitive true

(I'm surprised Jmol doesn't set that automatically; I thought it did)

and then refer to the author's chain designations.

load 1vu4.cif
print show('chains').join( )

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n 
o p q r s t u v w x y z 0 1 2

Bob


On Thu, Aug 14, 2014 at 3:11 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
How to select chains in large structures? Testing on Jmol.jar 14.2.4_2014.08.03 
 2014-08-03 08:56

We are working on 4v8m, one of the ‘large structures’ ( 
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/4v8m.cif.gz ) . The 
asymmetric unit for this structure is composed of multiple PDB entries: 3ZEQ, 
3ZEX, 3ZEY, 3ZF7 and has 86 chains.

The chain names are the following:
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,
U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,
JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,
WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,
JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,
WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC

The command getProperty chaininfo displays a long list, including the two 
character chains, which means to me that Jmol parses the mmCIF file and builds 
a data structure.

Selecting one character name chains (tested a few), report 0 atoms selected, 
like  select chain=‘A’. Some of the two character name chains also report 0 
atoms, like select chain=‘DA'

Several of the two character name chains return something, including those 
chains that are not reported in the list of chains! The file does not report 
chain AX nor AZ, but the select chain command finds atoms associated to that 
name.

$ select chain='AA'
47370 atoms selected
$ select chain='AB'
1557 atoms selected
$ select chain='AC'
1620 atoms selected
$ select chain='AD'
853 atoms selected
$ select chain='AE'
1300 atoms selected
$ select chain='AX'
1628 atoms selected
$ select chain=‘AZ’
526 atoms selected

Could it be that the internal structure index is wrong? Suggestions?

Jaim
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Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel

mail: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.ilhttp://oca.weizmann.ac.il/ (the protein 
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Proteopedia, http://proteopedia.orghttp://proteopedia.org/ (because life has 
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Re: [Jmol-users] bug fixes

[Jaime Prilusky]

On Aug 12, 2014, at 9:05 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
It was Chrome/Safari.
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.5_2014.08.12.zip
please test -- I would like to release this Friday.

Excellent. Testing on Mac OSX 10.9.4. Both parenthesis are Ok now.

Is confusing the old info in Jmol.properties, sowing up in Menu::About.

Thank you for fixing this,
Jaim

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Re: [Jmol-users] bug fixes

[Jaime Prilusky]

Jmol version 14.3.5_2014.08.09: unable to type open parenthesis '(' in JSmol 
Console. Closing parenthesis ‘)' is Ok.


On Aug 10, 2014, at 6:43 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.5_2014.08.09.zip
.

bug fix: CIF reader broken for load xxx.cif 1  (14.1.17_2014.06.07)
bug fix: CONTACT command not functioning properly with multiple models



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it is better to take what answer we get.

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Re: [Jmol-users] speedy testing requested

[Jaime Prilusky]

Testing now.

j2s/Jmol.properties states ___JmolVersion=14.2.2_2014.06.29 so it's difficult 
to know if the new version was loaded.

On quick test the loaded JSmol looks Ok.

Jaim

On Aug 2, 2014, at 5:45 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

I have just released Jmol 14.2.3 and would very very much appreciate some 
speedy testing before my workshop on Monday. It's actually a merge with Jmol 
14.3.3, so it has many new features, but among the bug fixes are:

bug fix: getProperty isosurfaceData fails
bug fix: move+moveto/zoomto still an issue.
bug fix: set pdbAddHydrogens incompatible with mmCIF */val
bug fix: write PDB fails
bug fix: Jmol application starts in English regardless of language
bug fix: 1-letter sequence for water showing as I not ?
bug fix: SHOW SEQUENCE FALSE not giving 1-letter sequences
bug fix: for (i in x)   where x is an associative array does not work
bug fix: DSSP analysis not returning information to console
bug fix: x.func(y) as second operand in a boolean and operation
 where the first operand evaluates to FALSE
 (so that x.func(y) is never evaluated), triggers a script error.
bug fix: set atomPicking, setDrawPicking, pickLabel, pickingSpinRate
 all should not be in state
bug fix: model kit menu does not allow setting of new element
bug fix: set atomPicking, setDrawPicking should not be in state
bug fix: getproperty structureInfo can fail with phosphorus monomers
bug fix: PDB reader not placing compoundSource in model auxiliary info

Bob


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Re: [Jmol-users] jmol-14.3.3_2014.07.29.zip

[Jaime Prilusky]

You’re right. On a simple page ( http://proteopedia.org/wiki/tests/sync2.html 
), ’sync * ON' works.

I will try to find out what’s interfering with this function on the original 
page.

Regards,
Jaim

On Jul 30, 2014, at 1:01 AM, Robert Hanson hans...@stolaf.edu wrote:

 Please send me a link to a nonfunctional page. I simply cannot reproduce this.
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Re: [Jmol-users] jmol-14.3.3_2014.07.29.zip

[Jaime Prilusky]

On 14.3.3_2014.07.29, the following fails in my tests to sync multiple applets, 
both on JSmol and Java.

jmolCheckbox('sync * ON','sync * OFF','check to sync',false);

Other tested features are Ok.

Jaim

On Jul 24, 2014, at 9:10 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.3_2014.07.24.zip

is a pre-release update. 14.3.3 and 14.2.3 (synchronized) will be released next 
week, prior to the BCCE meetin. Please test!


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Re: [Jmol-users] jmol-14.3.3_2014.07.24.zip

[Jaime Prilusky]

On 14.2.3, the following fails in my tests to sync multiple applets, both on 
JSmol and Java.

jmolCheckbox('sync * ON','sync * OFF','check to sync',false);

Other tested features are Ok.

Jaim

On Jul 24, 2014, at 9:10 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.3_2014.07.24.zip

is a pre-release update. 14.3.3 and 14.2.3 (synchronized) will be released next 
week, prior to the BCCE meetin. Please test!


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Re: [Jmol-users] is there a way to undisplay Jmol_S on the applet?

[Jaime Prilusky]

simply frank off should also work.

Jaim

On Jun 18, 2014, at 1:04 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 On 06/18/2014 11:50 AM, Ravi Raja Merugu wrote:
 Hello everyone,
 
 Is there a way i can undisplay Jmol_S logo on the viewer  in the right
 bottom, Is there any option like set frank off/false like the one used to
 be in Jmol-13x. I can give full credentials to the Jmol on the about
 section, but I just want to remove the Jmol_S text on the right bottom !!
 any way, to do so !! Help much appreciated.
 
 'set frank off' should still work.
 It works at least for me in JSmol 14.0.5 on this example page in our 
 Jena3D viewer: 
 jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=4otbAPPLET=html5
 
 Which version did you try and did you use the Java or the 
 HTML5/Javascript version?
 
 Regards,
 Rolf
 
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[Jmol-users] JSmol write protected Console?

[Jaime Prilusky]

From my server with Jmol 14.2.0_2014.06.13 and 14.0.17_2014.06.09 , the lower 
panel of Console from JSmol applet is write protected, i.e. can’t type 
commands to be executed.

On Jmol 14.1.16 it was Ok. Can others reproduce this?

Jaim

  *   14.2.0_2014.06.1
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Re: [Jmol-users] is there a way to undisplay Jmol_S on the applet?

[Jaime Prilusky]

Nameserver is unable to translate 
www.rsquarelabs.comhttp://www.rsquarelabs.com into a valid IP address
Can you provide the IP of the server?

Jaim

On Jun 18, 2014, at 1:53 PM, Ravi Raja Merugu 
raviraja.mer...@gmail.commailto:raviraja.mer...@gmail.com wrote:

Yes, the url is correct, I rechecked the address, it's publicly available and 
I'm able to access it !!, its http://www.rsquarelabs.com/bmv  im able to access 
it from india, I'm not sure if this domain is blocked in your place !!(thats 
unlikely though!). Please tell me if you still cant access the website !!

regards,
Ravi


On 18 June 2014 16:11, Rolf Huehne 
rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote:
On 06/18/2014 12:23 PM, Ravi Raja Merugu wrote:
 Interesting !! set frank off works on your site,, but I see that you are
 using jsmol.min.js, but im loading JsmolCore.js, JsmolApplet.js etc. Is
 that the rreason ? anyways ,. i will try with Jsmol.min.js and see..
 http://rsquarelabs.com/bmv . this is my website where i couldnt set the
 frank off.

The server at the web address you provided above couldn't be found.
Is the address correct or is the server not publicly available?

Regards,
Rolf
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Postdoc

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

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de
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Tax Number: 162/141/08228


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Re: [Jmol-users] WebGL support in OS X Yosemite

[Jaime Prilusky]

Dear Henry,

WebGL does make a big difference. You may test how Jmol renders on WebGL by 
adding use=webgl to a Proteopedia URL, as in the following examples

http://proteopedia.org/w/1d66?use=webgl
http://proteopedia.org/w/HIV-1_protease?use=webgl

As I understand, not all the potential of Jmol is available on WebGL at this 
time.

Jaim
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RD Bioinformatics and Data Management
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eml: jaime.prilu...@weizmann.ac.il
fax: 972-8-9344113
tel: 972-8-9344959

OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)

On Jun 3, 2014, at 5:38 PM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:

 http://learningwebgl.com/blog/?p=6368  announce that  OS X Yosemite will 
 support  WebGL.
 
 Could someone remind me whether this will be supremely immaterial to  JSmol, 
 or make a big difference, or something in between?
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Re: [Jmol-users] Jmol 14.1.14 released

[Jaime Prilusky]

On Apr 26, 2014, at 6:58 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14/

Was the release 14.1.14 removed from sourceforge.nethttp://sourceforge.net?

The latest version I’m able to access is 14.1.13

Jaim

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Re: [Jmol-users] jmol-14.1.12_2014.03.22.zip WHERE?

[Jaime Prilusky]

chemapps.stolaf.edu/jmol/zip/jmol-14.1.12_2014.03.22.zip

On Mar 23, 2014, at 6:55 PM, Eric Martz ema...@microbio.umass.edu wrote:

 I am getting file not found for the URL below.
 Someone please tell me where to get the current 14.1.12 -- thanks! Eric
 
 At 3/23/14, Robert Hanson wrote:
 http://chemapps.stolaf.edu/jmol-14.1.12_2014.03.22.ziphttp://chemapps.stolaf.edu/jmol-14.1.12_2014.03.22.zip
 
 SLOWLY uploading now
 
 Should fix the problems mentioned by Angel and Jaim as well as 
 others. These were introduced by my changing variable names. Sort of 
 knew that was going to be  more complicated than I thought
 
 Do please test and keep me posted.
 
 Bob
 
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 http://www.stolaf.edu/people/hansonrhttp://www.stolaf.edu/people/hansonr
 
 
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 it is better to take what answer we get.
 
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Re: [Jmol-users] jmol-14.1.12_2014.03.21.zip -- important update

[Jaime Prilusky]

On Mac 10.9.2, both Safari and Firefox 28.0, JSmol fails with message:

TypeError: 'undefined' is not an object (evaluating 
'this.stm.jmolStatusListener.isStereoSlave')

JSmol loads, able to open popup menu, no frank.

Java version, Jmol_S, works Ok.

Jaim

On Mar 22, 2014, at 2:05 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

Make that http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.12_2014.03.21b.zip

This has the full file set.


On Fri, Mar 21, 2014 at 3:12 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.12_2014.03.21.zip

Soon-to-be released as Jmol 14.0.12/14.1.12, this update fixes the bug Angel 
just reported, improves performance, and adds some pretty nifty  ZIP-file 
capabilities.

I decided that if I am adding features, I should also put time into reducing 
code size. So that's what I've been doing the past two days. Happy to report 
that despite those improvements, this version reduces the base load size by 43K 
(since last week), and the full package size by about 100K (since last year). 
In addition, my careful checking of what modules were being loaded and seeing 
what I could do about that means that PDB files will require about 200K less 
upon download, so they should load much faster. Mostly this is just be giving 
field variables more compact names, like this.mshttp://this.ms/ instead of 
this.modelSet (2K), this.ce instead of this.propertyColorEncoder (1.6K), 
etc. A little harder to decipher the code, but I can live with that.

With last week's 900% speed-up in molecular isosurface creation in Java (about 
300% in HTML5), the performance is really coming along. Every time I test JSmol 
it seems to be faster and smoother and more Java-like. Sure has come a long way 
in a year and a half. Very satisfying!

Fixes since 3.17 include:

___JmolVersion=14.1.12_2014.03.21

bug fix: getProperty() function does not recognize a list as a variable and 
returns it as a string (Angel)

bug fix: Dsn6Reader.java misnamed, causing EDS map file load error
 in JavaScript only. (I did not know that was even possible!)
 (Dale Tronrud)


New features:

The real news is that now we have some very powerful PNGJ/ZIP capabilities. You 
can unpack PNGJ files and repack them, adding files if you like, and you can 
create and modify ZIP files -- in JavaScript, of course. Thanks to Chuck 
Shubert and Ivan Ceraj (MIT) for getting me going on that.

new feature: x= format(JSON, data)
  -- simple way to generate JSON code.

new feature: x = format(base64, data)
  -- creates base64-encoding of the data
  -- prepends the string with ;base64,

new feature; binary byte array
  -- from array(s) where s starts with ;base64,
  -- from binary associative arrays

new feature: binary associative arrays
  -- Any array containing $_BINARY_$ as a key.
  -- Values may contain raw byte array data, but need not.
  -- Can be expanded or changed, just like any associative array.
  -- Seen in string form when in a string context.
  -- .type of elements will report byteArray

new feature: x = write(PNGJ)
  -- Creates a binary associative array equivalent to writing a PNGJ file
  -- Contains keys _IMAGE_, JmolManifest.txt, state.spt
 and all associated files.

new feature: write VAR x filename
or   write @x filename
  -- Where x is a binary array or a binary associative array.
  -- When x is a binary array, writes binary data to a file.
  -- When x is an array, creates a ZIP file
 (or PNGJ file, if _IMAGE_ is present and is PNG format),
 automatically converting strings starting with ;base64, to
 byte arrays in the ZIP file. To do the same with x a binary
 array, just use @{array(x)} instead of @x.

new feature: x = load(myfile,true)
  -- Creates a binary associative array variable x that contains the contents of
 the file file.
  -- data are stored as raw bytes.
  -- If the file is a standard file, the key _DATA_ will hold the file data.
  -- If the file is a PNGJ file, the key _IMAGE_ will hold the image data,
 and additional files are keyed by file name.
  -- If the file is a zip file, the files are keyed by file name.
  -- Note that x = load(myfile) without true loads the contents of
   the file into x and, if the file is a PNGJ or ZIP file, just loads
   the list of files in the collection, not the actual data.


Actually, the really really interesting news is that the reorganizing of the 
code that I am doing is making for capabilities that go way beyond Jmol. Want 
to create Zip files for any purpose? You can do that. Pull an image out of a 
Word document? Sure. Want to create PDF files from data on a web page? Have 
that.

That's because the way this works, I've basically produced a JavaScript library 
that can do anything Java can do. Very interesting...

Have a good weekend. I'm taking a break!

Bob





--
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Larson-Anderson Professor of Chemistry
St. Olaf College

Re: [Jmol-users] JSmol broken on Mac Safari back button

[Jaime Prilusky]

Otis,

Thank you for the suggestions.
Looking into that,

Jaim

On Jan 30, 2014, at 8:46 PM, Otis Rothenberger 
osrot...@chemagic.commailto:osrot...@chemagic.com wrote:

Jaim,

I see the same thing you are seeing on Bob's page. But...

Interesting point: I don't see any of this problem on my site - Safari, cross 
domain or within domain:

http://chemagic.com/JSmolVMK2.htm

After above load, location box = chemagic.comhttp://chemagic.com/ followed by 
back button reloads JSmol

The only thing I can think is that it might be related to one of the page/Jmol 
loaded calls that I use:

1) body onload=
2) JSmol ready function
3) JSmol structure loaded callback

Maybe also, server setting related to caching???


Otis

--
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o...@chemagic.commailto:o...@chemagic.com
http://chemagic.com




On Jan 30, 2014, at 11:57 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:

Thank you for the additional testing and suggestions.

I tested now on Chrome Version 32.0.1700.102, same Mac, and it works great: no 
freezing. I had the idea that Safari and Chrome shared a lot of internal code, 
but it seems that their behaviour with objects is different.

The freezing, of course, also happens on other sites using JSmol, like 
http://chemapps.stolaf.edu/jmol/jsmol/simple.htm

Jaim


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[Jmol-users] JSmol broken on Mac Safari back button

[Jaime Prilusky]

Is there a way to force loading JSmol when loading/rendering a page? JQuery 
should be able to do this.

This is why we might need to start with a fresh loaded JSmol: When clicking a 
‘back to previous page’ button on On Mac 10.9.1, Safari 7.0.1, JSmol renders 
non-operational. On Firefox 26.0, same Mac, it works Ok.

To test (better than the previous explanation):

1. go to http://proteopedia.org/w/3rec

2. verify if JSmol is working, ie mouse rotates model, zooms, etc.

3. go to another page by clicking a link, like ‘About Proteopedia’ in the 
bottom mid section

4. click on the browser’s ‘back to previous page’ button to display again the 
page 3rec

5. verify if JSmol is working, ie mouse rotates model, zooms, etc.

The main difference is that Firefox actually reloads JSmol on page back. Safari 
simply tries to work with what’s available, rendering a broken applet.

Jaim
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Re: [Jmol-users] JSmol broken on Mac Safari back button

[Jaime Prilusky]

Thank you for the additional testing and suggestions.

I tested now on Chrome Version 32.0.1700.102, same Mac, and it works great: no 
freezing. I had the idea that Safari and Chrome shared a lot of internal code, 
but it seems that their behaviour with objects is different.

The freezing, of course, also happens on other sites using JSmol, like 
http://chemapps.stolaf.edu/jmol/jsmol/simple.htm

Jaim

On Jan 30, 2014, at 5:20 PM, Otis Rothenberger 
osrot...@chemagic.commailto:osrot...@chemagic.com wrote:

Jaim,

I see what you're seeing with Safari.

Just to add a data point to the discussion, when I use the location box to 
navigate to another site (e.g. Google.comhttp://google.com/), the back button 
does force a reload of JSmol on your page.

When I try this same location box approach with:

http://proteopedia.org/wiki/index.php/Proteopedia:Structure_Index

The back button still does not reload JSmol - i.e. unlike going to 
Google.comhttp://google.com/

Maybe within the same domain, Safari simply goes to cache without supporting 
files when you use the back button???

You could prevent browser page caching with meta tags. You can also do this 
with JavaScript by defining an empty unbeforeunload function. I was never sure 
if either of these affected supporting files, however. I'm not sure you want to 
go this route. JSmol in user cache is a big plus.

Otis
--
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o...@chemagic.commailto:o...@chemagic.com
http://chemagic.com




On Jan 30, 2014, at 3:32 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:

Is there a way to force loading JSmol when loading/rendering a page? JQuery 
should be able to do this.

This is why we might need to start with a fresh loaded JSmol: When clicking a 
‘back to previous page’ button on On Mac 10.9.1, Safari 7.0.1, JSmol renders 
non-operational. On Firefox 26.0, same Mac, it works Ok.

To test (better than the previous explanation):

1. go to http://proteopedia.org/w/3rec

2. verify if JSmol is working, ie mouse rotates model, zooms, etc.

3. go to another page by clicking a link, like ‘About Proteopedia’ in the 
bottom mid section

4. click on the browser’s ‘back to previous page’ button to display again the 
page 3rec

5. verify if JSmol is working, ie mouse rotates model, zooms, etc.

The main difference is that Firefox actually reloads JSmol on page back. Safari 
simply tries to work with what’s available, rendering a broken applet.

Jaim
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Re: [Jmol-users] Where's my ATP?

[Jaime Prilusky]

I'm looking for the equivalent to getProperty ligandInfo that will return the 
complete list of names in HET or HETAM


definitely:
boolean isHetero = line.startsWith(HETATM);



On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
select hetero
?


On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Thank you Angel for the explanation. Still looking for a solution.

Jaim
On Jan 22, 2014, at 5:00 PM, Angel Herráez 
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:

 I'm guessing, but ATP may be recognized as nucleic by Jmol
 algorithm and hence excluded from the ligand set, which is not
 protein, not nucleic, not solvent if I remember correctly

 Sorry, ligand used to be hetero and not solvent, but the problem may
 be along those lines.



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St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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[Jmol-users] Where's my ATP?

[Jaime Prilusky]

getProperty ligandInfo returns a nice list of elements in the HET record of the 
PDB file, with some exceptions, like ATP and ADP. 

Those are not included in the ligandInfo report. Tested on Jmol 14.0.7 (both 
Java and HTML5) on several structures, including 1s22 and 1php

Is there other getProperty I can use to retrieve all the HET elements?

Where’s my ATP? 

Jaim
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Re: [Jmol-users] Where's my ATP?

[Jaime Prilusky]

Thank you Angel for the explanation. Still looking for a solution.

Jaim
On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote:

 I'm guessing, but ATP may be recognized as nucleic by Jmol 
 algorithm and hence excluded from the ligand set, which is not 
 protein, not nucleic, not solvent if I remember correctly
 
 Sorry, ligand used to be hetero and not solvent, but the problem may 
 be along those lines.
 
 
 
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Re: [Jmol-users] display echo while calculating

[Jaime Prilusky]

This might explain the erratic behaviour. It seems to work now and then, with 
not clear pattern.

Eve the simple example by Angel at 
http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not 
working. It will freeze while calculating, render the surface, and maybe draw 
and erase the message in a fast sequence.

set echo top center;
echo Calculating surface...;
refresh;
isosurface mySurface molecular;
echo;

Jaim

On Jan 15, 2014, at 7:03 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

echo and refresh will certainly work for this. But realize that there is no 
updating it, because the calculation is not interruptable at all, including 
updating any such message.


On Wed, Jan 15, 2014 at 6:18 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
I would like to have a message “Working …” while Jmol is calculating and 
rendering.

The following script displays the message only while rendering.

There’s no message while calculating. I’ve added some refresh commands just in 
case, but same result.

Tried with different representations instead of dots. Isosurface solvent is the 
worst example, where there seems to be no activity at all for a long time, then 
in a fast sequence I get the message, the rendering, and the message removed.

select all;
set echo middle center;
echo Working ...|Please wait;
font echo 20 ariel;
color echo green;
refresh;
dots 100%;
refresh;
set echo OFF;

Suggestions?


On Jan 13, 2014, at 3:25 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

That's right, too. In this case you are putting a script into the queue and 
then immediately and independently firing the alert message. Your initial way 
is correct; just add a REFRESH command prior to that if you want the model to 
be displayed during the alert.


On Mon, Jan 13, 2014 at 6:21 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Even if adding refresh to Jmol.script, the alert happens before the model gets 
loaded:

Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;');
alert(“Back”);

Jaim

On Jan 13, 2014, at 2:03 PM, Angel Herráez 
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:

 I agree that the use of refresh is often needed; that's my
 experience, in many occasions it's been key.

 However, the doc says otherwise:
 http://chemapps.stolaf.edu/jmol/docs/#refresh

 (Unnecessary, and thus deprecated.)

 I would remove that phrase, Bob :)




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it is better to take what answer we get.

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Re: [Jmol-users] display echo while calculating

[Jaime Prilusky]

Rolf: Thank you for testing on other browsers and platforms. While developing I 
stay on Mac.

Bob: I hope that this detailed report might help you find a solution for the 
problem.

Jaim

On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 On 01/16/2014 06:14 PM, Jaime Prilusky wrote:
 This might explain the erratic behaviour. It seems to work now and then, 
 with not clear pattern.
 
 Eve the simple example by Angel at 
 http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is 
 not working. It will freeze while calculating, render the surface, and maybe 
 draw and erase the message in a fast sequence.
 
 Since you used 'Jmol' in your earlier posts in this thread I assumed you 
 were referring to the Java version. But since you are now using 'JSmol 
 console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 
 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5).
 
 I can see the same behaviour there as you reported it if I invoke the 
 command 'isosurface solvent'. But it seems to have a clear browser 
 dependent pattern:
 
 With Chromium 31 on Linux the Please wait... message is never 
 displayed before the isosurface is calculated.
 
 With Firefox 26 on Linux the Please wait... message is displayed 
 before the isosurface is calculated the first time the command is 
 invoked after page load. Any further time it is not.
 
 Another browser-specific difference is that Firefox is totally 
 unresponsive during the isosurface calculation while Chromium stays 
 responsive.
 
 Regards,
 Rolf
 
 -- 
 
 Rolf Huehne
 Postdoc
 
 Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
 Beutenbergstrasse 11
 07745 Jena, Germany
 
 Phone:   +49 3641 65 6205
 Fax: +49 3641 65 6210
 E-Mail:  rhue...@fli-leibniz.de
 Website: http://www.fli-leibniz.de
 
   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
 Chairman of Board of Trustees: Dennys Klein
 
 VAT No: DE 153 925 464
 Register of Associations: No. 230296, Amtsgericht Jena
 Tax Number: 162/141/08228
 
 
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Re: [Jmol-users] display echo while calculating

[Jaime Prilusky]

Thank you for the new version.
I would say that now the sequence is as follows:

it starts calculating the surface, freezing the browser
then appears the message, draws, disappears the message.

The message should appear before starting the long calculation time.

Again, this is on Mac. Maybe other platforms behave better.
Jaim

On Jan 16, 2014, at 9:20 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip

--- should fix this refeshing problem.


On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
Yes, I think I found it. delay 0.01 should work even though refresh does not:

set echo top left
echo working...
delay 0.01

echo


Please try that; I'll also get refresh working. Testing now.



On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Rolf: Thank you for testing on other browsers and platforms. While developing I 
stay on Mac.

Bob: I hope that this detailed report might help you find a solution for the 
problem.

Jaim

On Jan 16, 2014, at 8:14 PM, Rolf Huehne 
rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote:

 On 01/16/2014 06:14 PM, Jaime Prilusky wrote:
 This might explain the erratic behaviour. It seems to work now and then, 
 with not clear pattern.

 Eve the simple example by Angel at 
 http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is 
 not working. It will freeze while calculating, render the surface, and maybe 
 draw and erase the message in a fast sequence.

 Since you used 'Jmol' in your earlier posts in this thread I assumed you
 were referring to the Java version. But since you are now using 'JSmol
 console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5
 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5).

 I can see the same behaviour there as you reported it if I invoke the
 command 'isosurface solvent'. But it seems to have a clear browser
 dependent pattern:

 With Chromium 31 on Linux the Please wait... message is never
 displayed before the isosurface is calculated.

 With Firefox 26 on Linux the Please wait... message is displayed
 before the isosurface is calculated the first time the command is
 invoked after page load. Any further time it is not.

 Another browser-specific difference is that Firefox is totally
 unresponsive during the isosurface calculation while Chromium stays
 responsive.

 Regards,
 Rolf

 --

 Rolf Huehne
 Postdoc

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

 Phone:   +49 3641 65 6205tel:%2B49%203641%2065%206205
 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210
 E-Mail:  rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de
 Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
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If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Re: [Jmol-users] display echo while calculating

[Jaime Prilusky]

Dear Bob,

On Safari Mac, with jsmol 14.1.6_dev_2014.01.16 , the notice while working 
performs great with delay 0.1 instead of refresh

Thank you for the suggestion.
Jaim

On Jan 16, 2014, at 10:10 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:

Thank you for the new version.
I would say that now the sequence is as follows:

it starts calculating the surface, freezing the browser
then appears the message, draws, disappears the message.

The message should appear before starting the long calculation time.

Again, this is on Mac. Maybe other platforms behave better.
Jaim

On Jan 16, 2014, at 9:20 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip

--- should fix this refeshing problem.


On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
Yes, I think I found it. delay 0.01 should work even though refresh does not:

set echo top left
echo working...
delay 0.01

echo


Please try that; I'll also get refresh working. Testing now.



On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Rolf: Thank you for testing on other browsers and platforms. While developing I 
stay on Mac.

Bob: I hope that this detailed report might help you find a solution for the 
problem.

Jaim

On Jan 16, 2014, at 8:14 PM, Rolf Huehne 
rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote:

 On 01/16/2014 06:14 PM, Jaime Prilusky wrote:
 This might explain the erratic behaviour. It seems to work now and then, 
 with not clear pattern.

 Eve the simple example by Angel at 
 http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is 
 not working. It will freeze while calculating, render the surface, and maybe 
 draw and erase the message in a fast sequence.

 Since you used 'Jmol' in your earlier posts in this thread I assumed you
 were referring to the Java version. But since you are now using 'JSmol
 console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5
 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5).

 I can see the same behaviour there as you reported it if I invoke the
 command 'isosurface solvent'. But it seems to have a clear browser
 dependent pattern:

 With Chromium 31 on Linux the Please wait... message is never
 displayed before the isosurface is calculated.

 With Firefox 26 on Linux the Please wait... message is displayed
 before the isosurface is calculated the first time the command is
 invoked after page load. Any further time it is not.

 Another browser-specific difference is that Firefox is totally
 unresponsive during the isosurface calculation while Chromium stays
 responsive.

 Regards,
 Rolf

 --

 Rolf Huehne
 Postdoc

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

 Phone:   +49 3641 65 6205tel:%2B49%203641%2065%206205
 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210
 E-Mail:  rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de
 Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/

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

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


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--
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Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




--
Robert M. Hanson
Larson

Re: [Jmol-users] display echo while calculating

[Jaime Prilusky]

I would say that this is not a delay caused by loading, unless modules or model 
get unloaded in the middle.

The Scene Authoring Tool in Proteopedia allows me to render and remove 
isosurface over and over again on the same loaded model with the click of a 
button. All components should be already available when requesting the same 
operation for a second or third time.

Besides, only using 'delay 0.1' instead of 'refresh' allows for the working 
message to appear at the expected times in the same overall structure. This is 
good enough for the purpose of keeping the user aware that something's going on.

Jaim

On Jan 17, 2014, at 4:12 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

nah. impossible.  I wonder if what you are seeing is the time it takes to load 
the modular components. If you have turned off the loading monitor, you may 
think nothing is happening -- or the calculation has started. I have a quite 
variable connection here in Jamaica (especially working through my VPN), and 
just now I saw very slow component loading while that command was processed.  
Take a look at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm -- middle 
column, half-way down: echo/surface test. I'm guessing the flash is the 
calculation. everything before that is file loading.

Bob


On Thu, Jan 16, 2014 at 3:10 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Thank you for the new version.
I would say that now the sequence is as follows:

it starts calculating the surface, freezing the browser
then appears the message, draws, disappears the message.

The message should appear before starting the long calculation time.

Again, this is on Mac. Maybe other platforms behave better.
Jaim

On Jan 16, 2014, at 9:20 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip

--- should fix this refeshing problem.


On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
Yes, I think I found it. delay 0.01 should work even though refresh does not:

set echo top left
echo working...
delay 0.01

echo


Please try that; I'll also get refresh working. Testing now.



On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Rolf: Thank you for testing on other browsers and platforms. While developing I 
stay on Mac.

Bob: I hope that this detailed report might help you find a solution for the 
problem.

Jaim

On Jan 16, 2014, at 8:14 PM, Rolf Huehne 
rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote:

 On 01/16/2014 06:14 PM, Jaime Prilusky wrote:
 This might explain the erratic behaviour. It seems to work now and then, 
 with not clear pattern.

 Eve the simple example by Angel at 
 http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is 
 not working. It will freeze while calculating, render the surface, and maybe 
 draw and erase the message in a fast sequence.

 Since you used 'Jmol' in your earlier posts in this thread I assumed you
 were referring to the Java version. But since you are now using 'JSmol
 console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5
 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5).

 I can see the same behaviour there as you reported it if I invoke the
 command 'isosurface solvent'. But it seems to have a clear browser
 dependent pattern:

 With Chromium 31 on Linux the Please wait... message is never
 displayed before the isosurface is calculated.

 With Firefox 26 on Linux the Please wait... message is displayed
 before the isosurface is calculated the first time the command is
 invoked after page load. Any further time it is not.

 Another browser-specific difference is that Firefox is totally
 unresponsive during the isosurface calculation while Chromium stays
 responsive.

 Regards,
 Rolf

 --

 Rolf Huehne
 Postdoc

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

 Phone:   +49 3641 65 6205tel:%2B49%203641%2065%206205
 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210
 E-Mail:  rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de
 Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/

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

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


 --
 CenturyLink Cloud: The Leader in Enterprise Cloud Services.
 Learn Why More Businesses Are Choosing CenturyLink Cloud For
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[Jmol-users] display echo while calculating

[Jaime Prilusky]

I would like to have a message “Working …” while Jmol is calculating and 
rendering.

The following script displays the message only while rendering.

There’s no message while calculating. I’ve added some refresh commands just in 
case, but same result.

Tried with different representations instead of dots. Isosurface solvent is the 
worst example, where there seems to be no activity at all for a long time, then 
in a fast sequence I get the message, the rendering, and the message removed.

select all;
set echo middle center;
echo Working ...|Please wait;
font echo 20 ariel;
color echo green;
refresh;
dots 100%;
refresh;
set echo OFF;

Suggestions?


On Jan 13, 2014, at 3:25 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

That's right, too. In this case you are putting a script into the queue and 
then immediately and independently firing the alert message. Your initial way 
is correct; just add a REFRESH command prior to that if you want the model to 
be displayed during the alert.


On Mon, Jan 13, 2014 at 6:21 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Even if adding refresh to Jmol.script, the alert happens before the model gets 
loaded:

Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;');
alert(“Back”);

Jaim

On Jan 13, 2014, at 2:03 PM, Angel Herráez 
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:

 I agree that the use of refresh is often needed; that's my
 experience, in many occasions it's been key.

 However, the doc says otherwise:
 http://chemapps.stolaf.edu/jmol/docs/#refresh

 (Unnecessary, and thus deprecated.)

 I would remove that phrase, Bob :)




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--
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Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Re: [Jmol-users] display echo while calculating

[Jaime Prilusky]

Thank you for a prompt reply, but it’s not working for me on 14.0.5.
The command waitmessage is undocumented. Maybe it’s something you added?

On Jan 15, 2014, at 1:48 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 On 01/15/2014 12:18 PM, Jaime Prilusky wrote:
 I would like to have a message “Working …” while Jmol is calculating and 
 rendering.
 
 The following script displays the message only while rendering.
 
 There’s no message while calculating. I’ve added some refresh commands just 
 in case, but same result.
 
 Tried with different representations instead of dots. Isosurface solvent is 
 the worst example, where there seems to be no activity at all for a long 
 time, then in a fast sequence I get the message, the rendering, and the 
 message removed.
 
 select all;
 set echo middle center;
 echo Working ...|Please wait;
 font echo 20 ariel;
 color echo green;
 refresh;
 dots 100%;
 refresh;
 set echo OFF;
 
 Suggestions?
 
 The same approach seems to work properly within the 'Jena3D Viewer' with 
 Jmol 14.0.1 (e.g.: 
 http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1otzAPPLET=java).
 There each command string that is issued with 'Jmol.script()' is 
 surrounded by the following:
 
 BEFORE: 'set echo waitmessage 0% 100%; echo Please wait...; refresh;\n'
 
 AFTER: '\n set echo waitmessage off;'
 
 If you would enter in the 'Script' input field of the 'Jena3D Viewer' 
 interface for example select all; isosurface solvent then the command 
 string sent to Jmol would actually look like this:
 
 set echo waitmessage 0% 100%; echo Please wait...; refresh;\nselect 
 all; isosurface solvent\n set echo waitmessage off;
 
 The Please wait... message appears on my system while Jmol is 
 calculating the isosurface.
 
 Regards,
 Rolf
 
 -- 
 
 Rolf Huehne
 Postdoc
 
 Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
 Beutenbergstrasse 11
 07745 Jena, Germany
 
 Phone:   +49 3641 65 6205
 Fax: +49 3641 65 6210
 E-Mail:  rhue...@fli-leibniz.de
 Website: http://www.fli-leibniz.de
 
   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
 Chairman of Board of Trustees: Dennys Klein
 
 VAT No: DE 153 925 464
 Register of Associations: No. 230296, Amtsgericht Jena
 Tax Number: 162/141/08228
 
 
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[Jmol-users] display echo while calculating WORKING Ok

[Jaime Prilusky]

Please disregard previous mail. Your suggestion of using waitmessage works 
perfect.
Thank you again,
Jaim

On Jan 15, 2014, at 3:06 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il 
wrote:

 Thank you for a prompt reply, but it’s not working for me on 14.0.5.
 The command waitmessage is undocumented. Maybe it’s something you added?
 
 On Jan 15, 2014, at 1:48 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:
 
 On 01/15/2014 12:18 PM, Jaime Prilusky wrote:
 I would like to have a message “Working …” while Jmol is calculating and 
 rendering.
 
 The following script displays the message only while rendering.
 
 There’s no message while calculating. I’ve added some refresh commands just 
 in case, but same result.
 
 Tried with different representations instead of dots. Isosurface solvent is 
 the worst example, where there seems to be no activity at all for a long 
 time, then in a fast sequence I get the message, the rendering, and the 
 message removed.
 
 select all;
 set echo middle center;
 echo Working ...|Please wait;
 font echo 20 ariel;
 color echo green;
 refresh;
 dots 100%;
 refresh;
 set echo OFF;
 
 Suggestions?
 
 The same approach seems to work properly within the 'Jena3D Viewer' with 
 Jmol 14.0.1 (e.g.: 
 http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1otzAPPLET=java).
 There each command string that is issued with 'Jmol.script()' is 
 surrounded by the following:
 
 BEFORE: 'set echo waitmessage 0% 100%; echo Please wait...; refresh;\n'
 
 AFTER: '\n set echo waitmessage off;'
 
 If you would enter in the 'Script' input field of the 'Jena3D Viewer' 
 interface for example select all; isosurface solvent then the command 
 string sent to Jmol would actually look like this:
 
 set echo waitmessage 0% 100%; echo Please wait...; refresh;\nselect 
 all; isosurface solvent\n set echo waitmessage off;
 
 The Please wait... message appears on my system while Jmol is 
 calculating the isosurface.
 
 Regards,
 Rolf
 
 -- 
 
 Rolf Huehne
 Postdoc
 
 Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
 Beutenbergstrasse 11
 07745 Jena, Germany
 
 Phone:   +49 3641 65 6205
 Fax: +49 3641 65 6210
 E-Mail:  rhue...@fli-leibniz.de
 Website: http://www.fli-leibniz.de
 
  Scientific Director: Prof. Dr. K. Lenhard Rudolph
   Head of Administration: Dr. Daniele Barthel
 Chairman of Board of Trustees: Dennys Klein
 
 VAT No: DE 153 925 464
 Register of Associations: No. 230296, Amtsgericht Jena
 Tax Number: 162/141/08228
 
 
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[Jmol-users] Jmol.script() not returning

[Jaime Prilusky]

We used to have a call to javascript as part of the script text, but that is 
not longer working:

Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’);

On the following example, the alert() happens before the script gets executed. 
The threading mechanism plays here against us. 

Jmol.script(jmol0,'load data/123.pdb; select all; color blue;');
alert(“Back”);

Suggestions? The set (callback) mechanism doesn’t seem to be the right choice.

Jaim
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[Jmol-users] platformSpeed on mouse zoom

[Jaime Prilusky]

It would be good for set platformSpeed to apply also when zooming in or out the 
model.
It does work as advertised on rotation.

Jaim
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[Jmol-users] platformSpeed on mouse zoom CORRECTION

[Jaime Prilusky]

On 14.0.5 , rendering with HTML5, set platformSpeed works perfect when the 
zooming action is driven by shift-cursor up/down.
It does not work when zooming with the mouse wheel.

Jaim
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Re: [Jmol-users] Jmol.script() not returning

[Jaime Prilusky]

Dear Bob,
Can you please give me an example on how to call a javascript function after 
the Jmol.script() is done?
Thank you in advance,
Jaim

On Jan 13, 2014, at 1:55 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

It's not that the alert is coming first; it's that there is no REFRESH before 
the alert. If you had that command prior to the  javascript command, then the 
structure will appear before the alert.

I would argue that this is proper behavior. There is no particular reason to 
demand an automatic refresh prior to a javascript command, and the behavior is 
the same for both Java and HTML5 modes.

Bob




On Mon, Jan 13, 2014 at 5:12 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
We used to have a call to javascript as part of the script text, but that is 
not longer working:

Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’);

On the following example, the alert() happens before the script gets executed. 
The threading mechanism plays here against us.

Jmol.script(jmol0,'load data/123.pdb; select all; color blue;');
alert(“Back”);

Suggestions? The set (callback) mechanism doesn’t seem to be the right choice.

Jaim
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Re: [Jmol-users] Jmol.script() not returning

[Jaime Prilusky]

Even if adding refresh to Jmol.script, the alert happens before the model gets 
loaded:

Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;');
alert(“Back”);

Jaim

On Jan 13, 2014, at 2:03 PM, Angel Herráez angel.herr...@uah.es wrote:

 I agree that the use of refresh is often needed; that's my 
 experience, in many occasions it's been key.
 
 However, the doc says otherwise:
 http://chemapps.stolaf.edu/jmol/docs/#refresh
 
 (Unnecessary, and thus deprecated.)
 
 I would remove that phrase, Bob :)
 
 
 
 
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Re: [Jmol-users] Jmol.script() not returning

[Jaime Prilusky]

Have you tried it on 14.0.5 with HTML5?

Jaim

On Jan 13, 2014, at 2:26 PM, Otis Rothenberger 
osrot...@chemagic.commailto:osrot...@chemagic.com wrote:

I use the javascript command frequently. From past experience, arguments in 
functions can cause issues. At a minimum, I would put quotes around the 
javascript itself. I think this has to be rigged so that these are double 
quotes - i.e. javascript alert('Hey there!') This means changing your quote 
structure in the whole Jmol script.

One thing that made issues go away for me completely is to simply use a 
function without an argument. That function, when called, can do anything you 
need done after the Jmol script executes.

Otis


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On Jan 13, 2014, at 7:03 AM, Angel Herráez 
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:

I agree that the use of refresh is often needed; that's my
experience, in many occasions it's been key.

However, the doc says otherwise:
http://chemapps.stolaf.edu/jmol/docs/#refresh

(Unnecessary, and thus deprecated.)

I would remove that phrase, Bob :)




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Re: [Jmol-users] platformSpeed on mouse zoom CORRECTION

[Jaime Prilusky]

On Jan 13, 2014, at 7:03 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
 I know why that is, but I have to think about how to change the behavior. It's 
not trivial.

Not critical. It can wait.

What happens on iPad? Does the pinch-to-zoom gets recognised by platformSpeed ? 
Just curious.

Jaim


On Mon, Jan 13, 2014 at 7:02 AM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
On 14.0.5 , rendering with HTML5, set platformSpeed works perfect when the 
zooming action is driven by shift-cursor up/down.
It does not work when zooming with the mouse wheel.

Jaim

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Re: [Jmol-users] JSmol menu doesn't open

[Jaime Prilusky]

Are you in any way disabling or capturing events from mouse right-click ?

Jaim

On Jan 7, 2014, at 5:56 PM, Eric Martz ema...@microbio.umass.edu wrote:

 I cannot seem to get the JSmol menu to open in 14.0.3 e.g.
 
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 
 Any suggestions?
 
 Eric
 
 
 
 
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Re: [Jmol-users] Jmol 14.x.4 released

[Jaime Prilusky]

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.4
Not much here, but one important fix for ribbons, so if you do anything with 
proteins be sure to download this modification in 14.0 and 14.1.
Bob

Thank you.

Fixed the misplaced rockets elements.

PSE conversion works smooth, no problems reported at 
http://ispcsrv.weizmann.ac.il/a2jmolb/browse

Best Regards,

Jaim
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[Jmol-users] 14.0.3 misplaced elements rockets

[Jaime Prilusky]

Jmol 14.0.3 shows misplaced elements when requesting rockets representation on 
3STU

Try the following, on either Jmol.jar or JmolApplet:

file - get PDB - 3STU
Select - All
Style - Structures - Rockets

Jmol version 13.2.8 renders Ok.
Jmol 14.0.3 shows misplaced elements.

Jaim
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[Jmol-users] jvxlInvalidatedVertexData on show isosurface for 14.1.3

[Jaime Prilusky]

The line containing jvxlInvalidatedVertexData still appears on Jmol 14.1.3

An email from June 2012 reports this as a bug to be fixed, but the problem 
persists on several Jmol versions after 13.0.1

‘jvxlInvalidatedVertexData' appears as an additional line when requesting ‘show 
isosurface’ on recent Jmol versions. It was not present on Jmol 13.0.1

The sequence of commands below, on Jmol 13.0.1, generates a valid JVXL string. 
On recent versions it also contains the jvxlInvalidatedVertexData additional 
data, which seems to affect subsequent loading of the JVXL string.

load 3rec;
isosurface solvent;
show isosurface;

Jaim

__
Dr Jaime Prilusky
Head Bioinformatics 
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel

mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)



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Re: [Jmol-users] isosurfaceData as JVXL string

[Jaime Prilusky]

Thank you. This works perfect.
Jaim

On Dec 29, 2013, at 9:47 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

Have a desired isosurface as the current isosurface -- if necessary, use

  isosurface ID 

by itself to select.

Then issue:

show isosurface


From JavaScript, you could use:

var xmlData = Jmol.evaluate(jmolApplet0, script('show isosurface'))




On Sat, Dec 28, 2013 at 1:31 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
What's the correct syntax to get from JSmol applet the isosurface data as JVXL 
string in javascript?

I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0, 
isosurfaceData) could do.

Thank you in advance,

Happy Holidays,
Jaim




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[Jmol-users] isosurfaceData as JVXL string

[Jaime Prilusky]

What's the correct syntax to get from JSmol applet the isosurface data as JVXL 
string in javascript?

I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0, 
isosurfaceData) could do.

Thank you in advance,

Happy Holidays,
Jaim




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[Jmol-users] isosurfaceData as JVXL string

[Jaime Prilusky]

What's the correct syntax to get from JSmol applet the isosurface data as JVXL 
string in javascript?

I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0, 
isosurfaceData) could do.

Thank you in advance,

Happy Holidays,
Jaim



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Re: [Jmol-users] Platform-specific switch Java/HTML5

[Jaime Prilusky]

On Dec 12, 2013, at 6:19 PM, Robert Hanson hans...@stolaf.edu wrote:
 It's still there. Should work. RCSB uses this. Proteopedia, I think.

On Proteopedia we use MobileDetect.php ( http://mobiledetect.net ) to send back 
to the user a proper configuration based on the platform.

It seems that checking for Java can't go undetected and it generates the java 
disabled yellow applet report.

Jaim
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Re: [Jmol-users] PHP server

[Jaime Prilusky]

Dear Charles,

You are welcome to create and host your pages at http://proteopedia.org

We have material from several courses and also provide environment for students 
to do their practices and prepare their own work. Some examples at 
http://proteopedia.org/w/Student_Projects .

Proteopedia includes a friendly scene editor that might help you in preparing 
your interactive pages.

Pages you may want to browse are 
http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators%27_Pages 
, http://proteopedia.org/w/Help:Contents , 
http://proteopedia.org/w/Teaching_Strategies_Using_Proteopedia 

Please feel free to write if you have questions or need any help.

Regards,

Jaim
__
Dr Jaime Prilusky
Head Bioinformatics 
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel

mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)


On Dec 11, 2013, at 6:59 AM, Charles Gasser csgas...@ucdavis.edu wrote:

 I am a naïve user who takes the sample pages and modifies them to my purposes 
 with only minimal understanding of what is actually involved under the 
 hood.  While note necessary for pages where I just show  some structures (e. 
 g. this page I made: 
 http://www.mcb.ucdavis.edu/courses/jsmol/aapages/Aliphatic.html), all pages 
 that I construct that include scripts that alter structures only work if I 
 include a call to jmol.php.  Unfortunately, I do not have a PHP server I can 
 use at my location.  I saw that pages at multiple locations made use of 
 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;.  So I copied this and have 
 been using this in my pages that have selectable scripts (e. g. 
 http://www.mcb.ucdavis.edu/courses/jsmol/Nucleosomejs.htm ).
 
 I am not sure that using this site is appropriate.  So first I ask Robert if 
 it is okay for me to have my pages access this site that he setup at his 
 institution.  Second I ask about the persistence of this site as all of my 
 pages with scripts will break if this site changes its name or evaporates.
 
 Finally am I wrong?  Can scripts be done without making use of the PHP code?
 
 I am having a great time with JSmol and am recruiting others to make 
 additional useful pages.
 
 Thanks for your help!
 
 Chuck Gasser
 ==
 Charles S. Gasser
 Professor
 Dept. of Molecular and Cellular Biology
 University of California, Davis
 1 Shields Ave.
 Davis, CA  95616
 
 104 Briggs Hall
 530 752-1013
 
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Re: [Jmol-users] local testing ready iteration 1,203,304,440

[Jaime Prilusky]

Rolf,

Maybe the way I work on Proteopedia might help you.

I have a CGI script that sends the content of the structure files to 
Jmol/JSmol: getlateststructure

The script gets as a parameter the name of the file to return or the PDB id for 
that file, and looks for the ending “.gz” on that parameter. This “.gz” ending 
gets removed from the actual name of the requested data and kept as a flag of 
the type of data required. No additional CGI parameter is required.

If the “.gz” flag is present then the script will do whatever its necessary to 
get the data and send it gzipped. Otherwise it will send it uncompressed. This 
is, depending on the request, the script will uncompress compressed files 
before sending, or will compress plain data, to keep the receiving applet happy.

Jaim

On Dec 2, 2013, at 2:20 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 On 12/01/2013 09:42 PM, Robert Hanson wrote:
 On Thu, Nov 28, 2013 at 12:12 PM, Rolf Huehne rhue...@fli-leibniz.dewrote:
 If someone could tell me a way to convince browsers to uncompress
 gzip-compressed CGI output before feeding it into JSmol I would be happy
 to implement it.
 
 I think your server is not set up to deliver gzipped files automatically.
 Perhaps?
 
 The problem whith this is here that the file content is served by a CGI 
 script instead of a static file. As far as I could find out the Apache 
 web server configuration options don't seem to be usable in this case.
 And switching to direct file serving is not really an option for me.
 
 I am working on a way to mimic it by the CGI script but it doesn't work yet.
 
 There might be an additional more general way (not only for standard 
 compressed binary files) to avoid sending the data three times involving 
 a PHP script. A CGI script could serve the binary data directly encoded 
 as base64 without the need for an additional PHP script and two 
 additional data transfers.
 
 I think there would be needed two configurable options for this:
 
 1) A special CGI binary mode indicator in the file URL (like the '.bin' 
 file extension). In my case this could be for example cgi-bin/idb_send.pl.
 
 2) A special parameter attached to the CGI URL, e.g. ENCODING=base64 
 by JSmol.
 
 Option 2) would prevent that base64 encoding would have to be done also 
 with Java although it wouldn't be necessary there. Since the actual 
 'Jena3D Viewer' CGI script (3d_mapping.pl) doesn't know in advance if 
 Java or HTML5 will be chosen by the client it would be better to add the 
 'ENCODING' parameter only if necessary on the client side by JSmol.
 
 Regards,
 Rolf
 
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 Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
 Beutenbergstrasse 11
 07745 Jena, Germany
 
 Phone:   +49 3641 65 6205
 Fax: +49 3641 65 6210
 E-Mail:  rhue...@fli-leibniz.de
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Re: [Jmol-users] Please test (2)

[Jaime Prilusky]

On Nov 27, 2013, at 12:30 AM, Robert Hanson hans...@stolaf.edu wrote:
 Yes, it's related to the fact that BondSet is an inner class of Bond. 
 Something is as happening out of order. Utlimately, Bond.BondSet is created 
 just fine. Very curious!

Found in your code a few other calls to Clazz.superConstructor( that would 
generate a non-existing file path, like it happens with J.modelset.Bond.BondSet

Are these working Ok? If this is the case, then why?

J.jvxl.calc.MarchingSquares.ContourVertex
J.jvxl.readers.Dsn6BinaryReader
JSV.source.JSVXmlReader.DataBuffer
JZ.Inflate.Return

Jaim
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Re: [Jmol-users] Please test (2)

[Jaime Prilusky]

The “Bond/BondSet.js” error appears also on Mac Firefox 25.0.1, but the applet 
continues working. You may see error reports with Firebug.

This might come from lines like this one in Bond.js and other files:

J/modelset/Bond.js:Clazz.superConstructor (this, J.modelset.Bond.BondSet, []);

The call to superConstructor assumes that J, modelset and Bond are directories, 
while BondSet is a file with the ‘.js’ extension.

Jaim


On Nov 26, 2013, at 12:02 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

The Bond/BondSet.js message is certainly curious, but it's not a show 
stopper. This appears even on web-site access via Safari. The message just 
after that is the killer, having to do with not being able to load core.z.js. 
Safari (like Chrome or Firefox without special settings) will not allow access 
to local files.

The yellow box should be gone now for Safari hosted access to Jmol. The problem 
was that apparently Safari is no longer accepting the object tag. The 
applet tag is required so that you can click on the windows and accept the 
website for the applet. Must be a bug, but I have switched JSmol to the applet 
tag when it detects Safari.

There is still a problem with local file reading. It looks to me as though 
Safari is not recognizing local JNLP applications within the browser. Or there 
is some setting we are missing.

Firefox is working fine for Safari local file access, so I concur with Phil and 
suggest we just write off Safari for now.

Bob


On Mon, Nov 25, 2013 at 9:09 AM, Philip Bays 
pb...@saintmarys.edumailto:pb...@saintmarys.edu wrote:
I meant this version of Safari, not this version of Jmol!!  Safari has lots of 
quirks right now, I think.  I still am not able to run jmol locally, because I 
get a Safari message that java is not enables, despite the fact that I have it 
enabled anyplace I can find to enable it.  But firefox works fine so that is 
what I will use for the time being.


On Nov 25, 2013, at 10:04 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

Anything you can send me would be helpful. I will test Safari locally here 
today and see what I can find.


On Mon, Nov 25, 2013 at 4:12 AM, Philip Bays 
pb...@saintmarys.edumailto:pb...@saintmarys.edu wrote:
Oh, yes.   I see them scroll by as the applet is loading and can see them using 
the SHOW link.  So we will just attribute this to a Safari flaw — like a lot of 
others in this version!!


On Nov 24, 2013, at 5:29 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

There should be a whole flood of messages in Jmol's Java console. (Behind the 
applet and visible with the Info SHOW link under the applet.) No?

Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edumailto:pb...@saintmarys.edu



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Re: [Jmol-users] Please test (2)

[Jaime Prilusky]

Thank you for this release. Runs Ok on Mac 10.9 FFox 25.0.1

Unable to convince Safari 7.0 to run a local applet.

Also tried with a Proteopedia exported page and (again FFox on Mac) it works 
great!!

Jaim


On Nov 24, 2013, at 8:47 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

Here's the file set that should run locally, possibly with no questions asked 
except a first one.

http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip

The test is to open test2.htm and click the signed applet link next to the 
applet.

And, of course, to try your own pages.

Bob




On Sat, Nov 23, 2013 at 10:44 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
Very pleased to report that we should have no problem with file:// based 
loading of Jmol and JSpecView java applets. In fact, now you don't need a 
browser to open them, either. The solution was to provide Java Network Launch 
Protocols in the directory containing the JAR files and to reference that with 
a jnlp-href attribute in the applet's object tag. Simple as that! Here is the 
Oracle developer forum answer that gave me the clue: 
https://forums.oracle.com/message/11256775#11256775

I must say, my hat is off to these guys. Java applets still rock. Hope to have 
files people can test tomorrow.


Bob





On Sat, Nov 23, 2013 at 7:45 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
Yes, OK, so Henry  found a catch.

I'm afraid this means no local access to Java applets. At least not in this 
iteration. In order to use Java applets on a local machine you will have to 
install a localhost web server.

Bummer for conferences.

I will complain.




On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S 
h.rz...@imperial.ac.ukmailto:h.rz...@imperial.ac.uk wrote:

On 23 Nov 2013, at 00:01, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

 Oops! That's the earlier link -- here's the new one:

 http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED



I downloaded JmolAppletSigned.jar  from  
http://chemapps.stolaf.edu/jmol/jsmol//java/

and used it locally.   It displayed a dialog  “Do you want to run this 
application”, indicated the publisher was  Integrated Graphics,  and the 
location was  file://

It then gave the yellow screen indicating  “This application will be blocked in 
a future …”.

I ticked the box “Do not show this again for apps from the publisher and 
location above” and proceeded but this then produced no Jmol output and an error

[Error] Failed to load resource: The requested URL was not found on this 
server. (JmolApplet.class, line 0)

From which  I take it that the appropriate  (Apache?) server response was not 
received which leads me to believe that one would have to run a local  http or 
https service to get this to work? Or is it that it cannot find the  
(relative? Absolute?) path to the  jar file?

But the odd thing is, as  I noted before,  if I used standard production Jmol 
(without a developer certificate), Jmol does load (although again with yellow 
box saying it might not work for future upgrades of  Java) and no error 
messages result.

so I guess installing the developer certificate has changed the underlying 
behaviour. The metaphor must be to trust only remote sites, and not a local one?

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Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




--
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Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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

[Jaime Prilusky]

Excellent. Will this also be true for the applet version?

In one year from now we’ll see if Java's still required, and, if the renewal 
requires a payment, find sources for that.

Jaim
__
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel

mail: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)


On Nov 3, 2013, at 10:57 AM, Nicolas Vervelle 
nverve...@gmail.commailto:nverve...@gmail.com wrote:

Hi Bob,

I know I have a full certificate, valid for one year, but it's unclear what I 
will have to do in one year : I'm not sure if renewal is still free or requires 
some money.
It's the only option I found that allowed me to have a free code signing 
certificate for the moment, so I decided to try it.
Users with recent Java version have now again the ability to trust my 
application once and for all, which is a lot better than what they were allowed 
with the self-signed certificate.

Nico


On Sun, Nov 3, 2013 at 12:51 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
hang in there. I think we will be ok. But, Nico, are you  sure you don't have a 
'trial version'


On Sat, Nov 2, 2013 at 2:20 PM, Nicolas Vervelle 
nverve...@gmail.commailto:nverve...@gmail.com wrote:
Hi Jonathan,

I think we can try using free certificates, I've got one 2 weeks ago from 
certum as they give them for free to open source developers.
I'm using it for a Java application, and it seems to work a lot better than 
with the self signed one.
If need be, I can sign a Jmol version with it to see if it works correctly with 
Jmol

Nico


On Sat, Nov 2, 2013 at 7:49 PM, Jonathan Gutow 
gu...@uwosh.edumailto:gu...@uwosh.edu wrote:
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.netmailto: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.edumailto: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.comhttp://intranet.example.com/) 
http://intranet.example.comhttp://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 Department
gu...@uwosh.edumailto:gu...@uwosh.edu
UW-Oshkosh  Office: 
920-424-1326tel:920-424-1326
800 Algoma Boulevard

Re: [Jmol-users] Using jsmol in MediaWikis

[Jaime Prilusky]

I'm currently improving and simplifying the JSmolExtension for MediaWiki I 
developed and currently using in Proteopedia.org.
Hope to release the new version next week. Please be patient.
Regards,
Jaim
__
Dr Jaime Prilusky
Head Bioinformatics 
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel

mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)


On Oct 10, 2013, at 11:02 AM, bir...@lachner-net.de wrote:

 Hi guys ...
  
 I'm using jmol extension for MediaWikis and I'm quite happy with it. But our 
 Wiki-Supporter wants to update to a new MediaWiki-Version - 1.2.1 as I 
 remember. They told that there are problems with the rendering. I don't have 
 the exact error message.
  
 So I told them, that may be Jsmol could be used in the Wiki that will even 
 solve the problem with tablets that read on the wiki. The guys had a look 
 around and found the Protopedia-Wiki and that they use Jsmol. See 
 http://proteopedia.org/wiki/index.php/Special:Version ... but no information 
 how they used Jsmol.
  
 And I found in the Mailinglist archieve that posting: 
 http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg21150.html
 I do not understand the instructions that are given there ...
  
 So ... is there any better instruction that can be given to our support-guys?
  
 Birgit
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Re: [Jmol-users] Jsmol: Problem downloading png/jmol

[Jaime Prilusky]

Add php to the file location. Change the path to /jmol/jsmol/php/jsmol.php

Jaim

On Sep 17, 2013, at 1:57 PM, björn bjoern-oliver.goh...@charite.de
 wrote:

 Hello,
 
 i use jsmol on my website.
 Everthing works fine but i cannot download the view anymore (as png or jsmol).
 
 I changed nothing.
 
 I got the following error message: 
 Not Found
 
 The requested URL /jmol/jsmol/jsmol.php was not found on this server.
 
 Apache Server at chemapps.stolaf.edu Port 80
 
 Can sombody help me?
 
 Best thanks
 Björn Gohlke
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Re: [Jmol-users] Recommendations for Jmol web hosting

[Jaime Prilusky]

Art,

Have you considered http://proteopedia.org ?

Jaim

On Sep 18, 2013, at 12:42 AM, Cox, Arthur G. wrote:

 I'd like to publish a few web pages with Jmol applets, but don't necessarily 
 want to use my own computer.
 
 Does anyone have a recommendation for a hosting company that supports java 
 applets?
 
 Should I be using a signed applet?
 
 Thanks
 -Art
 
 - Arthur G. Cox, PhD
 Associate Professor, Pharmaceutical Sciences
 South University School of Pharmacy
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 Phone: 912-201-8133 (office), 912-656-0699 (cell)
 E-Mail: a...@southuniversity.edu
 
 
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[Jmol-users] Jmol 13.0.1 connect_atoms error

[Jaime Prilusky]

Is this structure not longer valid? We have several scripts using it in the 
past and things were Ok.

Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on 
previous versions of Jmol? On newer versions?

Jaim

data connect;
  connect_atoms
91  198040960.4 -2.501  hbond;
1705187240960.4 -2.974  hbond;
1722185340960.4 -2.543  hbond;
end connect_atoms;


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Re: [Jmol-users] Jmol 13.0.1 connect_atoms error

[Jaime Prilusky]

Thank you for the correct format.
Jaim

On Sep 17, 2013, at 3:03 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

what version did that work in?  Should be:

data connect_atoms
91  198040960.4 -2.501  hbond;
1705187240960.4 -2.974  hbond;
1722185340960.4 -2.543  hbond;
end connect_atoms;

This format is not documented; it was intended only for definition of the 
state. For reference, the columns are:

1 and 2 are the 0-based atom indices
3 is the coded bond type.
4 is the diameter of the connector
5 is the energy calculated for this bond (only relevant for hydrogen bonds)
6 is the human-readable meaning of the coded bond type (ignored)


Bob



On Mon, Sep 16, 2013 at 1:45 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Is this structure not longer valid? We have several scripts using it in the 
past and things were Ok.

Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on 
previous versions of Jmol? On newer versions?

Jaim

data connect;
  connect_atoms
91  198040960.4 -2.501  hbond;
1705187240960.4 -2.974  hbond;
1722185340960.4 -2.543  hbond;
end connect_atoms;



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[Jmol-users] arbitrary hover string for each atom

[Jaime Prilusky]

Is there a way to set an arbitrary string for each atom to be displayed when 
hovering the atom? A real arbitrary string, not composed out of atom number, 
element, etc?

Jaim



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Re: [Jmol-users] arbitrary hover string for each atom

[Jaime Prilusky]

Hola Angel,

Thank you for a prompt reply. 

I was looking for an extension of the following way of setting properties for 
individual atoms. Besides spacefill and color, I would like to have an 
individual hover arbitrary string for each atom. 

select atomno=11; spacefill 4.00; color [xFF66FF]
select atomno=12; spacefill 16.00; color [xFF]

Regards,
Jaim

On Sep 1, 2013, at 12:05 PM, Angel Herráez angel.herr...@uah.es
 wrote:

 Hello Jaim!
 
 Yes, 
 hover This is an atom;
 
 but it applies to all atoms and I cannot find a way to make it selective
 
 Maybe my mapping your text into an atom property that is available to hover, 
 and then
 hover %[thatProperty]
 
 
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Re: [Jmol-users] arbitrary hover string for each atom

[Jaime Prilusky]

This looks interesting.
Thank you again,
Jaim

On Sep 1, 2013, at 1:06 PM, Angel Herráez angel.herr...@uah.es
 wrote:

 I found that hover can reflect the label text, and label can indeed be 
 assigned per atom.
 So, as long as you don't need to use labels, this seems to do the trick:
 
 hover %[label]; //affects all atoms
 select _N;
 label this is a nitrogen;
 set labelToggle {selected}; //turns label off without resetting it
 select _O;
 label this is an oxygen;
 set labelToggle {selected};
 select all;
 
 
 
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Re: [Jmol-users] bugs in version 13

[Jaime Prilusky]

On Jul 24, 2013, at 2:47 PM, Robert Hanson wrote:
OK, this is fixed.
http://chemapps.stolaf.edu/jmol-13.3.3_2013.07.24.zip

No visible side effects at http://ispcsrv.weizmann.ac.il/a2jmolb/browse

Jaim

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Re: [Jmol-users] a new logo-banner-icon for Jmol + JSmol

[Jaime Prilusky]

Very nice!! 
Jaim

__
Dr Jaime Prilusky
Head Bioinformatics 
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel

mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)


On May 13, 2013, at 1:13 PM, Angel Herráez angel.herr...@uah.es wrote:

 Hello Jmolers
 
 Saturday had an artistic flavor and today I am offering you a set of 
 new Jmol and JSmol logos or banners and an icon for the Jmol 
 application.
 
 http://biomodel.uah.es/Jmol/logos/
 
 If you like, you are welcome to use them in your pages.
 I am proposing this to be the official icon and logo for J(S)mol 
 13.1, if accepted it will soon go into the website and the Wiki (Home 
 page and Recycling Corner)
 
 Enjoy!
 
 Angel
 
 ·
 Dr. Angel Herráez
 Bioquímica y Biología Molecular, 
 Dep. Biología de Sistemas, Universidad de Alcalá
 28871 Alcalá de Henares  (Madrid)
 
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