[Jmol-users] labelPointer thickness

[Sérgio Ceroni da Silva]

Dear Jmol users/developers

Is there a way of increasing the thickness of label pointers?
Thanks
Sérgio



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Re: [Jmol-users] JSmol

[Sérgio Ceroni da Silva]

Em 24/07/2013 19:13, Angel Herráez escreveu:

Darren, quick solution:

I assume you were using Jmol.js

Then, find the jmolInitialize() call in your page, like

jmolInitialize("../../jmol-12.2.33");

and change it to

jmolInitialize("../../jmol-12.2.33", true);


Then open jsmol.zip in your downloaded Jmol 13, go to the "java" 
folder and extract all JmolAppletSigned*.jar files into your 
jmol-12-2-33 folder  --You can do that with either the old 12.2 files 
or the new 13.2 files --it probably will work in either case.


The page should now work as before, only using the signed applet


I'm a little bit confused: does that mean the line



should be removed from the html header?


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Re: [Jmol-users] accented characters

[Sérgio Ceroni da Silva]

Em 11/03/2013 06:45, Angel Herráez escreveu:
> Olá Sérgio
>
> This problem comes back from time to time, I thought we could be
> forgetting it.
>
> All depends on whether the browser knows the encoding of the
> JavaScript and JmolScript files.
>
> You are using the Java applet, not JSmol, right?
Hola Angel. Yes, I'm using the applet.

> First choice I would suggest is to make sure that all html pages have
> a proper declaration of charset in a meta tag.
All pages have 

> Second it to resave your script files as utf-8 (no need to replace
> the characters, just use a text editor that marks the file properly;
> I have used Notepad++ successfully).
Already tried that using Notepad++, encoding in UTF-8 with and without 
BOM. No success.




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[Jmol-users] accented characters

[Sérgio Ceroni da Silva]

Dear Jmol users/developers

I've just upgraded from 12.2.34 to 13.0.13 and all accented characters 
in script files (echo) are displaying like boxes.
After a quick search in the list I've found that a possible solution 
would be to change all accented characters to Unicode.
Is there a simpler solution?
Thanks
Sérgio



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Re: [Jmol-users] JSmol - three months in

[Sérgio Ceroni da Silva]

Em 24/11/2012 16:32, Robert Hanson escreveu:
> Please let me know if with Firefox you are seeing the alert "Firefox 
> bug -- continuing" at test2.htm

Yes (FF 17.0, Win7/64)


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Re: [Jmol-users] Rendering in POV-Ray broken in 12.2.0

[Sérgio Ceroni da Silva]

Em 14/10/2011 00:45, Robert Hanson escreveu:
> works fine for me in 12.2.1 and 12.2.0. Maybe it's some other problem 
> on your machine?

Just reinstalled POV-Ray 3.6.2:
- 12.0.49: OK
- 12.2.0: crash in pvengine64.exe while parsing tokens
- 12.2.1: crash in pvengine64.exe while parsing tokens

The *.pov file generated by 12.0.49 is considerably different from 
12.2.0 and 12.2.1 (which are identical).

Trying to load and render *.pov from 12.2.0 and 12.2.1 into POV-Ray 
generates loads of:
...
Parse Warning: Degenerate triangle. Please remove.
File: D:\Sergio_docs\Jmol_12.2.0.pov  Line: 1221
Parse Warning: Degenerate triangle. Please remove.
File: D:\Sergio_docs\Jmol_12.2.0.pov  Line: 1221
Parse Warning: Degenerate triangle. Please remove.
File: D:\Sergio_docs\Jmol_12.2.0.pov  Line: 1221
...


POV-Ray apears to be stuck here:

1219 #macro r(X1,Y1,Z1,X2,Y2,Z2,X3,Y3,Z3,R,G,B,T)
1220  triangle{,,
1221   pigment{rgbt}
1222   translucentFinish(T)
1223   clip()
1224   check_shadow()}
1225 #end


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[Jmol-users] Rendering in POV-Ray broken in 12.2.0

[Sérgio Ceroni da Silva]

Works fine in 12.0.49

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Re: [Jmol-users] Jmol 12.1.11 test

[Sérgio Ceroni da Silva]

  Em 10/09/2010 13:34, Angel Herráez escreveu:
> Sérgio,
> Java security policy has grown less tolerant in the last months,
> particularly for Firefox. Are you sure your other scripts currently
> still work, in the same Java+browser version?
Absolutely sure. Just run locally each and every one of them!
Using all the latest versions: Firefox 3.6.9, java 1.6.0_21-b06, Win7 64
Same thing happens with IE 8.0.7600.16385
I'll carefully check whether there are any differences between the ones 
that work and the two that don't.
Very odd indeed.

> Check out
> http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local#Examples_of_folder_arrangement
I'm using the correct folder arrangement.

> http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local#Activating_UseCommandThrea
UseCommandThread did the trick with the two reluctant pages

Still, I'm intrigued why all the other pages are working fine but these two.

Many thanks Angel


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Re: [Jmol-users] Jmol 12.1.11 test

[Sérgio Ceroni da Silva]

> You can't access ../anything with the applet locally. Always been that way.

Strange. I have 30 other similar scripts working exactly this way. Can't 
figure out why this particular one doesn't.



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Re: [Jmol-users] Jmol 12.1.11 test

[Sérgio Ceroni da Silva]

 Em 10/09/2010 12:36, Robert Hanson escreveu:

applet or Jmol application?

2010/9/10 Sérgio Ceroni da Silva <mailto:sergio.cer...@ufrgs.br>>


Em 10/09/2010 02:58, Robert Hanson escreveu:

This one is for Rich, Eric, Jay, Sergio, and Oliver.

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


Many thanks. Works fine with the navy color now.
However (there is allways one), I've found another strange
behavior. It happens in version 11 too (still trying to determine
when it started)...



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Re: [Jmol-users] Jmol 12.1.11 test

[Sérgio Ceroni da Silva]

Another little thing. Just found out TRANSLUCENT changed form a maximum 
of 8 to 6 but the documentation still has:


/Starting with Jmol 11.2, TRANSLUCENT can take an integer in the range 
0-6 (indicating eighths -- 0, 1/*8*, 2/*8*, etc.)/


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Re: [Jmol-users] Jmol 12.1.11 test

[Sérgio Ceroni da Silva]

 Em 10/09/2010 02:58, Robert Hanson escreveu:

This one is for Rich, Eric, Jay, Sergio, and Oliver.

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


Many thanks. Works fine with the navy color now.

However (there is allways one), I've found another strange behavior. It 
happens in version 11 too (still trying to determine when it started).

I have this script file (a01.txt)
script ../../JmolFiles/aviso.txt
load ac.pdb
spacefill off
wireframe off
spin on
select protein
wireframe 100
color cpk

calling this one (aviso.txt)
zap
set echo middle center
font echo 18 sanserif bold
color echo [x26476B]
echo Carregando a molécula||Isso pode levar alguns 
segundos,|dependendo da complexidade da|molécula e da velocidade da 
conexão||Aguarde...

delay 1.0

The problem is they don't work locally (Win7 64bit), meaning all 
commands are ignored after that first line in a01.txt. They do work when 
uploaded to the server!
It doesn't seem to be a problem with the slash because I have some other 
similar scripts that work just fine and changing to a \ didn't make any 
difference.


When the first line in a01.txt is commented out then it works fine. That 
would indicate a problem in the second script file (aviso.txt). But (and 
this is very odd) when all commands in this second script file are 
commented out the simple action of calling it breaks all subsequent 
commands in the first script file.

No idea where/how to start debugging this thing!
Thanks in advance.
Sérgio

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[Jmol-users] possible bug in 12.0.x

[Sérgio Ceroni da Silva]

  Hello, since I've upgraded from 11.8.26 to 12.0.x my scripts stopped 
working.
One of the problems I found was the echo command: "echo color navy;" 
doesn't work and breaks all following commands in the script (solved by 
changing to the hex value, but I think "navy" is a valid javascript color).
Still debugging some other scripts. I'll report back when (if) I find 
the offending command.
Thanks in advance
Sérgio

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Re: [Jmol-users] Chime to Jmol

[Sérgio Ceroni da Silva]

Em 22/04/2010 20:21, Robert Hanson escreveu:
> I thought Chime was gone, but in preparing a chapter I'm writing I 
> found quite a few sites out there that still use Chime and, of course, 
> are mostly useless now.

To my surprise I found out a few weeks ago that Symyx released a new 
Chime version last January. According to them "Symyx® Chime 2.6 SP8 
provides the following improvements from the previous versions: Support 
for Microsoft® Internet Explorer 7 (IE7) and Internet Explorer 8 (IE8); 
Support for Windows 7, Windows Vista SP2 and Windows XP SP3; Support for 
Office 2007; Option to launch Symyx® Draw instead of ISIS/Draw; Support 
for silent (no prompt) installations."

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[Jmol-users] alpha transparency not working

[Sérgio Ceroni da Silva]

Not sure if it is a general issue but alpha transparency doesn't appear 
to be working on 11.8.22.
I'm using Pov-ray 3.6.2 on Windows 7 64-bit.

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Re: [Jmol-users] bug in "select"

[Sérgio Ceroni da Silva]

Just noticed that 11.4.6 has the old bug where H1, H2 and H3 from DNA 
bases are selected as backbone.

Did it resurface or the fix was applied only to 11.5.x ?

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[Jmol-users] Bug in 11.5.46

[Sérgio Ceroni da Silva]

There appears to be a bug in 11.5.46: after a spin command the molecule 
is resized and centered in an erroneous way, off axis.

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[Jmol-users] Bug in export to pov-ray

[Sérgio Ceroni da Silva]

I've sent this e-mail before but apparently it didn't reach the list.

There is a bug in the export to pov-ray option. Pov-ray halts with a 
parse error:


File: D:\Sergio_docs\Jmol.pov  Line: 3236
File Context (5 lines):
}
face_indices { 1224, <611,578,612> //
, <611,578,612,645>
*Parse Error: Vector expected but color expression found.*
Total Scene Processing Times
 Parse Time:0 hours  0 minutes  0 seconds (0 seconds)
 Photon Time:   0 hours  0 minutes  0 seconds (0 seconds)
 Render Time:   0 hours  0 minutes  0 seconds (0 seconds)
 Total Time:0 hours  0 minutes  0 seconds (0 seconds)
CPU time used: kernel 0.08 seconds, user 0.56 seconds, total 0.64 seconds
POV-Ray finished

It happens in 11.5.40, .41 and .42.
11.4.4 works fine.

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[Jmol-users] bug in Export to POV-Ray

[Sérgio Ceroni da Silva]

I'm getting an error when trying to render on POV-Ray 3.6.1:
Parse Error: Vector expected but color expression found.

It happens in 11.5.40, .41 and .42.
11.4.4 works fine.

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Re: [Jmol-users] bug in "select"

[Sérgio Ceroni da Silva]

version=11.5.40
# bug fix: H1 and H3 in DNA are NOT backbone

H1 from bases in 1JVE and H2 in 1Z04 still showing up. 1CGP now is fine.
Doubt: is it the bug or a problem with the PDBs?

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Re: [Jmol-users] bug in "set antialiasdisplay"

[Sérgio Ceroni da Silva]

Bob Hanson wrote:
> That's certainly working in the very latest version I have.
>
> Sérgio Ceroni da Silva wrote:
>
>   
>> Has anyone noticed that after issuing a "set antialiasdisplay true" all 
>> the clickable echoes stop responding?
>> Regards
>> Sérgio

Maybe this is the case of an echoing e-mail :-D
The original message was sent April 24 and you replied "oops" 
(<http://sourceforge.net/mailarchive/forum.php?thread_name=4810E013.8010804%40cbiot.ufrgs.br&forum_name=jmol-users>)
It's working fine since then.
Thanks

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[Jmol-users] bug in "select"

[Sérgio Ceroni da Silva]

I think there is a bug in 11.5.38 and 11.5.39 (not sure when it started, 
but old versions didn't have it):
using "select dna and backbone" selects also some H from the DNA bases.
Tested on 1CGP, 1JVE, 1Z04.

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[Jmol-users] bug in "set antialiasDisplay"

[Sérgio Ceroni da Silva]

Has anyone noticed that after issuing a "set antialiasDisplay true" all 
the clickable echoes stop responding?
Regards
Sérgio

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[Jmol-users] bug in "set antialiasdisplay"

[Sérgio Ceroni da Silva]

Has anyone noticed that after issuing a "set antialiasdisplay true" all 
the clickable echoes stop responding?
Regards
Sérgio

-- 
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Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
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Re: [Jmol-users] Proteopedia: green links problem in Firefox

[Sérgio Ceroni da Silva]

Eric Martz wrote:
> 1. Please tell us: When you go to the main page of Proteopedia, before you 
> click a green link, does a molecule display in Jmol? If yes, do you see the 
> SCRIPTED view intended, which is a ribbon, colored by group (N->C rainbow), 
> with a magenta spacefilled ligand?
>   
Yes

> 2. Do the green links work for anyone who is using Firefox on Windows?
>   
Green links not working. Firefox 2.0.0.13, WinXP SP2, Java 1.6.0_05.

> 3A. Also please click on "Random Page" (in the navigation box at the upper 
> left) and try the green links under the molecule for Ligands and Sites. Does 
> every green link fail?
>   
All failed.

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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Re: [Jmol-users] differences in renderization

[Sérgio Ceroni da Silva]

Bob Hanson wrote:

Sérgio Ceroni da Silva wrote:
  
Dear Jmol users, I've noticed some differences in renderization between 
the applet and the application and I'm not sure if it is a bug or 
something related to the pdb file. This can be seen in 2NUU, using 
rocket or cartoon, around two beta-sheets (tyr51, chains G, H, I).

Regards
Sérgio

say more -- it could be two versions of Jmol, I suppose, but the applet 
and application can't possibly render anything differently -- they use 
exactly the same code.
  


Well, I was quite sure I was using the same version (RC10). Obviously 
not, since I cannot reproduce the problem anymore.

Thanks
Sérgio

--
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
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[Jmol-users] differences in renderization

[Sérgio Ceroni da Silva]

Dear Jmol users, I've noticed some differences in renderization between 
the applet and the application and I'm not sure if it is a bug or 
something related to the pdb file. This can be seen in 2NUU, using 
rocket or cartoon, around two beta-sheets (tyr51, chains G, H, I).
Regards
Sérgio

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309
http://www6.ufrgs.br/bioquimica
 



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Re: [Jmol-users] set shadow

[Sérgio Ceroni da Silva]

Bob Hanson escreveu:
> Sérgio Ceroni da Silva wrote:
> Hi everybody
> Today I found out that some old scripts were misbehaving with the latest 
> (11.4.RC2) Jmol (can't tell when it started). The command "set shadow off" 
> was the culprit (many commands stop responding after a "set shadow"). It 
> appears that this Rasmol/Chime command was never implemented (could find only 
> a few discussions dating back to 2004 on the mailing lists). Strangely, only 
> recent Jmol versions started to show this behaviour.
> Regards
> Sérgio
>
>   
>> That's because we made "set" function only with implemented Jmol 
>> parameters. So really this is a GOOD thing -- that it is indicating 
>> properly that "set shadow" doesn't exist

I'm deeply sorry if I didn't make myself clear. I wasn't complaining 
about the missing "set shadow". I was just reporting that I would expect 
for Jmol to ignore it and carry on with the remaining valid instructions 
in the script instead of the odd behaviour I've seen. Thought could be a 
symptom worth reporting, since an invalid command is affecting several 
other valid ones that follow in the script. Should this really be expected?

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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[Jmol-users] set shadow

[Sérgio Ceroni da Silva]

Hi everybody

Today I found out that some old scripts were misbehaving with the latest 
(11.4.RC2) Jmol (can't tell when it started).
The command "set shadow off" was the culprit (many commands stop 
responding after a "set shadow").
It appears that this Rasmol/Chime command was never implemented (could 
find only a few discussions dating back to 2004 on the mailing lists).
Strangely, only recent Jmol versions started to show this behaviour.
Regards
Sérgio

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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http://www6.ufrgs.br/bioquimica
 



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Re: [Jmol-users] [Jmol-developers] Jmol application freezing

[Sérgio Ceroni da Silva]

 >>Sérgio Ceroni da Silva wrote:
 >>
 >>Dear all
 >>I've been doing some testing regarding the problem where Jmol
 >>application freezes after a few changes in the default language.
 >>Apparently it's a memory matter. Every time the language is changed
 >>javaw uses more 6 to 15 MB. This happen with every language change until
 >>all resources are consumed. I hope this is not a java problem and a fix
 >>can be found.
 >>Regards
 >>Sérgio
 >>
 >
 >This is a Jmol problem, but I am not experienced enough to solve it.
 >Language switching is not intended to be done more than once or twice in
 >a single Jmol run. If you have to switch back and forth among languages,
 >consider restarting Jmol. That's just the way it is for now. Perhaps
 >someone knows how to track down the memory leak associated with this; I
 >tried for some time, and I give up. The viewer is not finalizing upon
 >creation of a new one, which is what language switching involves. I do
 >not know how to fix that.
 >
 >Bob

Hi Bob, thanks for your reply. I've come across this problem while 
checking the pt_br translation I did. I was going from en to pt_br and 
back again several times to make sure the translation was meaningful and 
not just literal. Sure no sane person will change languages more than a 
couple of times, so it is not a big problem. I've reported it just 
because I thought this memory leak could be a symptom of a more 
important problem.
Thanks again.
Sérgio



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[Jmol-users] Jmol application freezing

[Sérgio Ceroni da Silva]

Dear all
I've been doing some testing regarding the problem where Jmol 
application freezes after a few changes in the default language. 
Apparently it's a memory matter. Every time the language is changed 
javaw uses more 6 to 15 MB. This happen with every language change until 
all resources are consumed. I hope this is not a java problem and a fix 
can be found.
Regards
Sérgio

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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[Jmol-users] Suggestions

[Sérgio Ceroni da Silva]

 
How about including in the Jmol page something demonstrating its
applications and capabilities in different areas?
It would complement (or replace) the already existing animated display,
which is very good and thorough but with a (perhaps) too long script.
I would suggest something like the image bellow, with short (10-15s ?)
and representative scripts attached to each button. Everybody could
contribute with an eye-catching script to show-off Jmol put to action
in his/her field. This page could also replace the screenshot gallery
and function as a quick and updated reference to what can be done with
Jmol.


-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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http://www6.ufrgs.br/bioquimica
 


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Re: [Jmol-users] Not all chemicals are molecules

[Sérgio Ceroni da Silva]

Nick Greeves wrote:
Molecular structures is not accurate. Bob uses quartz as an example, 
there are lovely pages showing zeolites, graphite, diamond, ionic 
solids e.g. NaCl, metals, etc. etc. _*These are not molecules but  
they are chemicals*_.

Am I missing something?!

I don't think we should accept the idea that chemical is a "dirty" 
word. It is widely understood and appropriate.
I dont't think this discussion should be about how clean chemistry is 
but the more appropriate way to describe what Jmol does and how it can 
be used.



How about "Jmol - an open-source Java viewer for three-dimensional
chemical and biological structures" ?

A hand, a wing, a hair... they are all biological structures.
Again, I think this discussion shouldn't be about chemistry vs biology.

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Re: [Jmol-users] 11.1.42

[Sérgio Ceroni da Silva]

Bob Hanson wrote:
> We are decidedly closer to 11.2. Nico has just released 11.1.42. All 
> testing appreciated.
>   
Sometimes Jmol standalone freezes after changing language (WinXP, java 
1.6.0_01).
I've noticed that the image blinks during language change as if the 
molecule was being reloaded. Is that the normal behaviour?
Regards
Sérgio

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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http://www6.ufrgs.br/bioquimica
 



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Re: [Jmol-users] problem with old tutorial

[Sérgio Ceroni da Silva]

Bob Hanson escreveu:
I think it's a level of change none of us understand -- the cache I was 
referring to was the Java cache, which is where the JAR files go, which 
is different (sigh) from the "browser cache"; apparently that was not 
cleared. I've seen it happen, but I don't know exactly how to remedy it. 
Shouldn't be a major issue. Somehow the Java Virtual Machine gets messed 
up and tries to read the wrong set of JAR files.


Bob
In WinXP this cache is located in "C:\Documents and 
Settings\USERNAME\Application data\Sun\Java\Deployment\cache" and can be 
cleared through Start>Control Panel>Java>General>Settings. I've run into 
trouble with some java applications before (never with Jmol) and 
developed the habit of clearing this cache periodically.

Regards
Sérgio

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Re: [Jmol-users] what are the different applet files?

[Sérgio Ceroni da Silva]

Bob Hanson wrote:
> What a timely question! I was just drafting a message to users
>
> Jmol users:
>
> We were all a bit confused with the new file naming, so we've decided to
> rename the applet files again -- just to thoroughly confuse you.
> Actually, this is much better. What follows refers to Jmol 11.1.36.
>
> There are four distinct options that you can use when using the Jmol
> applet. The typical user would only use one of these; we recommend the
> first.
>
> JmolApplet0*.jar
> JmolApplet.jar
> JmolAppletSigned.jar
> JmolAppletSigned0*.jar
>
> (Note: * here is a wildcard character meaning "all files starting with".)
>   

I would suggest renaming the "README.txt" file to 
"READ_ME_RIGHT_NOW_OR_ELSE_ALL_YOUR_MOLECULES_WILL_BE_CURSED.TXT" >:o  
(just remember to update the text before the cursing :-) )

Seriously now: why not organizing the zip (tar, etc) file in directories:

/
COPYRIGHT.txt
LICENSE.txt
README.txt
|
+--Jmol
|  +--jmol
|  +--jmol.bat
|  +--Jmol.jar
|  +--jmol.mac
|  +--jmol.sh
|
+--Jmol_applet
+--Jmol.js
+--Signed
|  +--Multiple_files
|  |  +--JmolAppletSigned0*.jar
|  |  +-- ...
|  |  +-- ...
|  |
|  +--Single_file
| +--JmolAppletSigned.jar
|
+--Unsigned
   +--Multiple_files
   |  +--JmolApplet0*.jar
   |  +-- ...
|  |  +-- ...
   |
   +--Single_file
  +--JmolApplet.jar




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Re: [Jmol-users] Student Jmol pages

[Sérgio Ceroni da Silva]

Jeff Hansen wrote:
I taught a course on Enzyme Mechanisms for the first time this 
semester.  The course is an organic chemistry course that looks at the 
organic reaction mechanisms of enzyme reactions.  At the end of the 
semester the students did group presentations on a particular enzyme 
that is assigned to them.  I had them do the molecular visualization 
using Jmol and make a web page to go along with the presentation.  I 
thought some of you might be interested in seeing their work.  It 
isn't fantastic but not too bad for starting from zero and getting to 
this in 3 or 4 weeks.  The pages are at: 
http://people.depauw.edu/jhansen/Presentations/
Perhaps you should consider including them in Jmol Wiki 
(http://wiki.jmol.org:81/index.php/Websites_Using_Jmol).

Regards
Sérgio
<mailto:[EMAIL PROTECTED]>

--
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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Re: [Jmol-users] pt-br translation

[Sérgio Ceroni da Silva]

Nicolas Vervelle wrote:

Sérgio Ceroni da Silva wrote:
Just downloaded and tried it. Everything OK with the standalone. 
Couldn't test the applet though (found unfamiliar jar files there!).
In the last versions (recently), we changed the JmolApplet0.jar - 
JmolApplet6.jar splitting into a new splitting to help speed up applet 
loading (jars are loaded when they are needed).
In the same time, we changed the naming pattern so the different jars 
have meaningful names.

Great! It's really faster.
Just bugging a little bit: haven't you thought about moving the "Signed" 
to the end of the filename? Perhaps JmolAppletXXX_Signed.jar? (I wasn't 
paying attention and missed the Smiles and Viewer!)


Applet tested OK (although I definitively still have to improve some of 
the translation).

Regards
Sérgio

PS: in another bit of bugging, I've noticed that in the language 
selection menu appears "Portuguese (Brazil) (pt_BR)". It should be 
"Portugu_ê_s (Bra_s_il) (pt_BR)".


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Re: [Jmol-users] pt-br translation

[Sérgio Ceroni da Silva]

Nicolas Vervelle wrote:
> For the moment, I have taken the solution that's not modifying the 
> current pt translation, so I have added your translation as pt_BR.
> We can change this if you think an other option is better.
>   
I think that's just fine. Maybe the pt team resume working in the near 
future. Besides, I believe the language differences justify separate 
translations.

> I am releasing 11.1.35 so that a first version with pt_BR can be tested.
>   
Just downloaded and tried it. Everything OK with the standalone. 
Couldn't test the applet though (found unfamiliar jar files there!).

> The current pt_BR.po files contains 6 + 11 fuzzy translations.
These I wasn't sure about the best way to translate, so I thought I 
would just leave them as fuzzy for a while. Also, while testing the 
standalone I've found some words that could be better translated in the 
context of the menu. I'll go back to them as well.

Many thanks for your help.
Regards
Sérgio



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Re: [Jmol-users] language menu

[Sérgio Ceroni da Silva]

Angel Herraez wrote:
> If creating a separate new pt-BR is troublesome, I would suggest that 
> 1) the former translator is contacted, to see it (s)he is willing to maintain 
> the pt-PT translation 
> up-to-date
> 2) if not, Sérgio updates the existing pt localization file as he pleases (I 
> guess that for 
> Portuguese-speaking users, a Brazilian menu will be better than a 
> half-English menu)
> 3) find out how many Portuguese users around, their viewpoints to this 
> respect or their 
> willingness to contribute translations
>   
Sounds great to me (Portuguese is spoken by ~210 M, ~188 M in Brazil).
Regards
Sérgio

-- 
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Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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Re: [Jmol-users] language menu

[Sérgio Ceroni da Silva]

Bob Hanson wrote:
> I'm ready for people to test the language business again. Please try:
>   
Yes to all three tests, but (there is always a but) the menus are mixed 
en/pt. Maybe it's because they have not been completely translated (?).
While on the subject, there are some minor (and not so minor) 
differences between pt and pt-br that I think would justify having pt-br 
included in the localization. How can I help?
Cheers
Sérgio

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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Re: [Jmol-users] slab/depth in more than one direction

[Sérgio Ceroni da Silva]

Bob Hanson escreveu:
> Sérgio Ceroni da Silva wrote:
>
>> Alan Hewat wrote:
>>
>>> BTW, there is an example of nice javascript slider controls on
>>> http://www.blueshoes.org/_bsJavascript/components/slider/examples/example9.html
>>>  
>>>
>>> This could eventually be adapted to displaying such slabs/sub-volumes.
>>
>> They look really really nice, but are dependent on external image files.
>> Sometime ago I found a code for a pure JS slider control that I've 
>> sent to Angel. He said "I will try to set it up on Recycling corner 
>> and make a sample page (slab, color, bond thickness, the new 
>
> See, for example,
> http://www.stolaf.edu/depts/chemistry/gca/chart.htm?doChartExample(2)
>
> Code is in
> http://www.stolaf.edu/depts/chemistry/gca/scroller.js
Just perfect.

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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Re: [Jmol-users] color-mapping fails in 11.1.30

[Sérgio Ceroni da Silva]

Angel Herraez wrote:
> I've being mad all morning trying to get some surfaces color-mapped 
> by MEP. I've got the mep in a dx file, and it works correctly. 
> However, when I save to JVXL, I cannot recover the mapping, only get 
> a plain orange surface.
> In the end, it seems that it is a difference in the latest versions 
> (11.1.30 and 11.1.29 at least), since I test in 11.1.5 and it works.
I've noticed this too. All white surfaces in 11.1.28 went orange in 11.1.29.
PS: it seems the js slider wasn't that nice :-(
Cheers
Sérgio

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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http://www6.ufrgs.br/bioquimica
 



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Re: [Jmol-users] slab/depth in more than one direction

[Sérgio Ceroni da Silva]

Alan Hewat wrote:

BTW, there is an example of nice javascript slider controls on
http://www.blueshoes.org/_bsJavascript/components/slider/examples/example9.html 


This could eventually be adapted to displaying such slabs/sub-volumes.


They look really really nice, but are dependent on external image files.
Sometime ago I found a code for a pure JS slider control that I've sent 
to Angel. He said "I will try to set it up on Recycling corner and make 
a sample page (slab, color, bond thickness, the new transparency... who 
knows what else?) I'm sure some people will make good use of it."
Angel is probably working on this and soon it will be available as a 
nice JS function (like the color picker he made available on Wiki's 
Recycling Corner <http://wiki.jmol.org:81/index.php/Recycling_Corner>).

Regards
Sérgio

--
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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[Jmol-users] faster 11.1.29

[Sérgio Ceroni da Silva]

Dear all
Is it just my impression or 11.1.29 is running faster than its predecessor?!
One of the computers I use to test things is an old K6-500, 384 MB RAM 
with a grandmotherboard PCChips. Today I downloaded the new applet and 
after that all scripts and molecule animations are running visibly 
faster (and I do mean much faster) on this oversized calculator. 
Everything else, including JRE, wasn't changed.
Code optimization? Voodoo? Just curious!
Sérgio

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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http://www6.ufrgs.br/bioquimica
 



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Re: [Jmol-users] "Loading" message

[Sérgio Ceroni da Silva]

P.J. Carroll wrote:
> How do I get the Jmol applet to display a "Loading..." message? When 
> I load a series of unit cells, e.g., with the command:
>
>   load .cif {444 666 0}
>
> it, of course, can take quite a while to load the atoms, depending on 
> the size of the molecule. During this time, the user has no 
> indication that something is going on. It would be nice to display a 
> message.
>   

Very simple:

script pre.txt; load .cif {444 666 0}


and the script file:

###
# pre.txt #
###
zap;
set echo middle center;
font echo 18 sanserif bold;
color echo navy;
echo Loading molecule|It could take a while||Please wait...;
delay 0.1;


I'm not sure if the "zap" and "delay" are still needed.
Regards
Sérgio

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
Tel.: +55 (51) 3308-6091 | Fax: +55 (51) 3308-7309
http://www6.ufrgs.br/bioquimica
 




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[Jmol-users] simple js color picker

[Sérgio Ceroni da Silva]

Hi everybody

I've adapted a simple javascript color picker to use in my pages. I find 
it very useful for changing molecule and applet background color. It 
generates a horizontal table (5 rows x 25 columns)  or a vertical one 
(25 rows x 5 columns). Some parameters like cell width and height are 
hard-coded, but could be easily changed to variables. If there is enough 
interest it could be improved and included as a function in Jmol.js. 
Just a thought.
Best wishes
Sérgio

//
//  Molecule color picker
//
HexMoleculeColor = new Array('00', '66', '99', 'cc', 'ff');
TableMoleculeColorPicker = '';
for (greenMoleculeColorValue = 0; greenMoleculeColorValue < 5; 
greenMoleculeColorValue++){
//Use the next line for a HORIZONTAL table
TableMoleculeColorPicker += '';
for (redMoleculeColorValue = 0; redMoleculeColorValue < 5; 
redMoleculeColorValue++) {
//Use the next line for a VERTICAL table
//TableMoleculeColorPicker += '';
for (blueMoleculeColorValue = 0; blueMoleculeColorValue < 5; 
blueMoleculeColorValue++) {
FinalHexMoleculeColor = '#' + 
HexMoleculeColor[redMoleculeColorValue] + 
HexMoleculeColor[greenMoleculeColorValue] + 
HexMoleculeColor[blueMoleculeColorValue];
FinalJmolHexMoleculeColor = '[x' + 
HexMoleculeColor[redMoleculeColorValue] + 
HexMoleculeColor[greenMoleculeColorValue] + 
HexMoleculeColor[blueMoleculeColorValue] + ']';
TableMoleculeColorPicker += '';
}
//Use the next line for a VERTICAL table
//TableMoleculeColorPicker += '';
}
//Use the next line for a HORIZONTAL table
TableMoleculeColorPicker += '';
}
TableMoleculeColorPicker += '';
document.write(TableMoleculeColorPicker);


//
//  Applet background color picker
//
HexAppBgColor = new Array('00', '66', '99', 'cc', 'ff');
TableAppBgColorPicker = '';
TableAppBgColorPicker += 'default';
TableAppBgColorPicker += '';
for (greenAppBgColorValue = 0; greenAppBgColorValue < 5; 
greenAppBgColorValue++){
//Use the next line for a HORIZONTAL table
TableAppBgColorPicker += '';
for (redAppBgColorValue = 0; redAppBgColorValue < 5; 
redAppBgColorValue++) {
//Use the next line for a VERTICAL table
//TableAppBgColorPicker += '';
for (blueAppBgColorValue = 0; blueAppBgColorValue < 5; 
blueAppBgColorValue++) {
FinalHexAppBgColor = '#' + HexAppBgColor[redAppBgColorValue] 
+ HexAppBgColor[greenAppBgColorValue] + HexAppBgColor[blueAppBgColorValue];
FinalJmolHexAppBgColor = '[x' + 
HexAppBgColor[redAppBgColorValue] + HexAppBgColor[greenAppBgColorValue] 
+ HexAppBgColor[blueAppBgColorValue] + ']';
    TableAppBgColorPicker += '';
}
//Use the next line for a VERTICAL table
//TableAppBgColorPicker += '';
}
//Use the next line for a HORIZONTAL table
TableAppBgColorPicker += '';
}
TableAppBgColorPicker += '';
document.write(TableAppBgColorPicker);

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309
http://www6.ufrgs.br/bioquimica
 



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Re: [Jmol-users] codebasedirectory error

[Sérgio Ceroni da Silva]

Angel Herraez escreveu:
viewing the models. If the models are in a different directory I 
couldnt figure out how to get it to work. 



It will work as long as the models are together or below the Jmol jar 
files.


I could get it to work independently of model and jar location (Firefox 
only). Very useful for testing prior to uploading. Here is the trick:

- copy all JmolAppletSigned*.jar and rename to JmolApplet*.jar
- put this signed-applets-disguised-as-not-signed in the same directory 
as the JmolAppletSigned*.jar


To upload the server I use the JmolApplet*.jar (not signed) only.

--
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309
http://www6.ufrgs.br/bioquimica


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Re: [Jmol-users] tag in jmolMenu()

[Sérgio Ceroni da Silva]

Angel Herraez escreveu:

On 1 Apr 2007 at 20:09, Sérgio Ceroni da Silva wrote:
  
Has anyone ever (thought about || felt the need for) adding support for 
the HTML  tag in jmolMenu() function?



Hi Sérgio 
I have tried and it's easy to do with a small change in Jmol.js. Here is the mechanism, in 
case someone has any suggestions; if people find it OK, I will update Jmol.js soon.


Add the optgroup entry as one more element in the array that is passed to Jmol.js. The 
first element must be the caption for the group ("label" in HTML syntax); the second and 
(optional) third elements are not used.

Then add an extra element to signal the end of the group.
Example:
jmolMenu([
[null, " select ", "selected"],
["color cpk", "- CPK pattern", null],
["#optgroup", "... Color by: ", null],
["color structure", "- structure", null],
["color chain", "- chain", null],
["color group", "- group", null],
["#optgroupEnd", null, null],
["#optgroup", " Other colors: ", null],
["color formalcharge", "- electric charge", null],
["color amino", "- amino-acids", null],
["color shapely", "- nucleotides", null],
["#optgroupEnd", null, null]
]);

The key words are "#optgroup" and "#optgroupEnd" which must be used exactly so.
  


Great!

The only other way I could achieve this was by replacing this code:

jmolMenu([
   [null, "||| select |||", "selected"],
   ["color cpk", "- CPK", null],
   [null, "||| Color by: |||", null],
   ["color structure", "- structures", null],
   ["color chain", "- chains", null],
   ["color group", "- groups", null],
   ["color formalcharge", "- charge", null],
   ["color amino", "- amino acids", null],
   ["color shapely", "- nucleotides", null]
]);

with this one:

jmolHtml("onchange=\"jmolScript(this.options[this.selectedIndex].value);\">");

jmolHtml("||| select |||");
jmolHtml("");
jmolHtml("CPK");
jmolHtml("");
jmolHtml("");
jmolHtml("structures");
jmolHtml("chains");
jmolHtml("groups");
jmolHtml("charge");
jmolHtml("amino acids");
jmolHtml("nucleotides");
jmolHtml("");
jmolHtml("");

I had to use onchange inside  because IE doesn't support onclick 
inside  (when is MS going to follow international standards?!).

Obviously your solution is much better.
Many thanks
Sérgio



--
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309
http://www6.ufrgs.br/bioquimica


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[Jmol-users] tag in jmolMenu()

[Sérgio Ceroni da Silva]

Has anyone ever (thought about || felt the need for) adding support for 
the HTML  tag in jmolMenu() function?
I just ask because this tag helps organizing things when there are 
several options that could be grouped.
Many thanks
Sérgio



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Re: [Jmol-users] page design: flexible size, scrollable, no frames

[Sérgio Ceroni da Silva]

Angel Herraez wrote:
> Once again, today I have addressed the way to achieve a webpage design that:
> ...
> Up to now, I had only achieved this by using frames --which I still love, but 
> many people 
> cry loud at--
> ...
> I am very interested in feedback:
> - whether you find any advantages over your own designs
> - whether it works in your system, particularly Mac and Linux users
Great! Can't wait to try and adapt my pages.
I too don't understand what is the problem in using frames.
Works perfect on WinXP. Tomorrow I'll try on Linux (Fedora and Slack) 
and Solaris.
Thanks
Sérgio


-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309
http://www6.ufrgs.br/bioquimica
 



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Re: [Jmol-users] isosurfaces and the new translucency

[Sérgio Ceroni da Silva]

Timothy Driscoll escreveu:

I believe I've isolated the problem. Apparently, "select DNA" is not
working in 11.1.21. I've set up two pages:
 with 11.1.21
 with 11.0.1
They are identical except for the applet. Selecting DNA works fine on
the second.



hi,

I noticed this, too, and logged it as a bug a few days ago.
select nucleic should work instead, if you want a quick fix.
regards,
tim


Thanks. I'll change my scripts.
PS: congratulations to everyone involved in Jmol. It's really amazing 
what you've accomplished so far.


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Re: [Jmol-users] isosurfaces and the new translucency

[Sérgio Ceroni da Silva]

Bob Hanson wrote:
> Sergio, I'm not seeing this. What are you seeing that is "improper"?
>   

Frieda Reichsman wrote:
> Hi Sergio, 
>
> Are you actually issuing the command
>
> color translucent {object}
> as in,
> color translucent atoms?
>
> It should be: color {object} translucent
>
> If you are using scripts, this would render all subsequent commands  
> ineffective.

I believe I've isolated the problem. Apparently, "select DNA" is not 
working in 11.1.21. I've set up two pages:

 with 11.1.21

 with 11.0.1

They are identical except for the applet. Selecting DNA works fine on 
the second.


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Re: [Jmol-users] isosurfaces and the new translucency

[Sérgio Ceroni da Silva]

Frieda Reichsman wrote:
> I'm enjoying the beauty of the new translucency with surfaces...
I also enjoyed the translucent beauty of Jmol, but after a "color 
translucent X" commands like wireframe and spacefill cease to work properly.

-- 
Dr. Sérgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==
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http://www6.ufrgs.br/bioquimica
 



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