[Jmol-users] labelPointer thickness

Dear Jmol users/developers Is there a way of increasing the thickness of label pointers? Thanks Sérgio -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App inst

Re: [Jmol-users] JSmol

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 downlo

Re: [Jmol-users] accented characters

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? Ho

[Jmol-users] accented characters

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 solut

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

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) -- Monitor your physical, virtual and cloud in

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

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

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

Works fine in 12.0.49 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this d

Re: [Jmol-users] Jmol 12.1.11 test

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 t

Re: [Jmol-users] Jmol 12.1.11 test

> 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. -- Automate Storage Ti

Re: [Jmol-users] Jmol 12.1.11 test

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/

Re: [Jmol-users] Jmol 12.1.11 test

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.)/ --

Re: [Jmol-users] Jmol 12.1.11 test

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

[Jmol-users] possible bug in 12.0.x

t; 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 -- Prof. Sérgio Ceroni da Silva Laboratório de Biologia Molecular Aplicada - LBMA Faculdade de Veterinária - Universidade Federal do Rio Gran

Re: [Jmol-users] Chime to Jmol

ice 2007; Option to launch Symyx® Draw instead of ISIS/Draw; Support for silent (no prompt) installations." -- Prof. Sérgio Ceroni da Silva Laboratório de Biologia Molecular Aplicada - LBMA Faculdade de Veterinária - Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9090 P

[Jmol-users] alpha transparency not working

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. -- Prof. Sérgio Ceroni da Silva Laboratório de Biologia Molecular Aplicada - LBMA Faculdade de Veterinária - Universidade Federal do Rio Gra

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

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 ? -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 - Prédio

[Jmol-users] Bug in 11.5.46

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. -- 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

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

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. -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 -

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

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. -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves,

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

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? -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento

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

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 &

[Jmol-users] bug in "select"

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. -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade

[Jmol-users] bug in "set antialiasDisplay"

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

[Jmol-users] bug in "set antialiasdisplay"

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

Re: [Jmol-users] Proteopedia: green links problem in Firefox

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 Post

Re: [Jmol-users] differences in renderization

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, aroun

[Jmol-users] differences in renderization

io -- 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 | Fa

Re: [Jmol-users] set shadow

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 respon

[Jmol-users] set shadow

and 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

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

>>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 chan

[Jmol-users] Jmol application freezing

ources 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 -

[Jmol-users] Suggestions

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 == Tel.: +55

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

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

Re: [Jmol-users] 11.1.42

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 - Bras

Re: [Jmol-users] problem with old tutorial

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 t

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

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

Re: [Jmol-users] Student Jmol pages

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, Universid

Re: [Jmol-users] pt-br translation

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

Re: [Jmol-users] pt-br translation

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

Re: [Jmol-users] language menu

Portuguese is spoken by ~210 M, ~188 M in Brazil). 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 ==

Re: [Jmol-users] language menu

inor (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

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

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 >>> >>> &

Re: [Jmol-users] color-mapping fails in 11.1.30

nd, 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 C

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

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

[Jmol-users] faster 11.1.29

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 - P

Re: [Jmol-users] "Loading" message

## 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. Regar

[Jmol-users] simple js color picker

HexAppBgColor[blueAppBgColorValue]; FinalJmolHexAppBgColor = '[x' + HexAppBgColor[redAppBgColorValue] + HexAppBgColor[greenAppBgColorValue] + HexAppBgColor[blueAppBgColorValue] + ']'; TableAppBgColorPicker += ''; } //Use the next li

Re: [Jmol-users] codebasedirectory error

. -- 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

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

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 mech

[Jmol-users] tag in jmolMenu()

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 ---

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

ora 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

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

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

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

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 ar

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

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 Centr