Re: [Jmol-developers] Jmol in JS (and hopefully NextGen MW)

I don't think so. Why do you say that? All they have to do is provide changes to YOUR subsystem. What you describe is GPL. If they change the jmol code they must share those changes that they made to that code only not to their code. Am I wrong? Sent from my stupid iPhone On Oct 14, 2012, a

Re: [Jmol-developers] Java-less Jmol == "JSmol"

Dan, how are you? I'm happy to see you are still on the list. I'd love to talk with you some time. What's a good time to call you? Bob Sent from my stupid iPhone On Oct 13, 2012, at 2:12 PM, Dan Gezelter wrote: >> >> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm >> >> Consider it alp

Re: [Jmol-developers] Java-less Jmol == "JSmol"

I'll answer other questions when I'm at a real computer. Sent from my stupid iPhone On Oct 13, 2012, at 5:53 AM, Egon Willighagen wrote: > On Sat, Oct 13, 2012 at 6:21 AM, Robert Hanson wrote: >> Today I can point you to a not-exactly-fully-functional version of Jmol (we >> are calling it J

Re: [Jmol-developers] Java-less Jmol == "JSmol"

It's important to understand that this preliminary implementation depends on WebGL being operative. We don't have the autoswitching enabled. Tablets do not have WebGL. The iPad has it but it is crippled, presumably because if it were enabled it would make the iTunes store and apps in general

Re: [Jmol-developers] Forward of moderated message

Are you doing this in eclipse? Or using Jmol.jar? Are you doing the compiling? Maybe you are not getting clean compiling. Please try it at http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm You can just drag drop files into that. Sent from my stupid iphone On May 20, 2012, at 3

Re: [Jmol-developers] Can Jmol be embedded in other program?

will try to find more information about it. > Thanks very much. > > Regards, > Moon > > 2012/1/15 Angel Herráez > Hi Moon > > I'm not a programmer, so I cannot really give you a firm advice. > > Being different programming languages, the bets are not good. &g

[Jmol-developers] Jmol android part 3

http://www.youtube.com/watch?v=D7uOkhoJ0Oc Sent from my stupid iphone -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a

[Jmol-developers] Jmol android part 2

http://www.youtube.com/watch?v=JPwvCmD5IDg Sent from my stupid iphone -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a

[Jmol-developers] Jmol android

http://www.youtube.com/watch?v=og-lXFnDU-w Sent from my stupid iphone -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a

Re: [Jmol-developers] (no subject)

First we need to know about logging on to sourceforge. I doubt it has to do withEclipse. In the mean time just keep sending me patches. Sent from my stupid iphone On Oct 13, 2011, at 12:45 PM, Jonathan Gutow wrote: > Hmm...I was under the impression that Bob already checked that you have

Re: [Jmol-developers] Jmol 12.2.0 ready for release

Ok. Well, I was thinking I would move those back anyway. Don't do anything until I get a chance to do that. Sent from my stupid iphone On Oct 2, 2011, at 10:22 AM, Nicolas Vervelle wrote: > Hi, > > I was sailing the last few days, so unable to check the problem. I'm > answering from my mobi

Re: [Jmol-developers] autoBond and the .jmol/properties file

Great. Did you remember to fix both 11.6 & 11.7? Sent from my iPhone On Apr 14, 2009, at 4:01 PM, pim schravendijk wrote: Hi, I remembered I had svn login and committed my bug fix to svn. I hope it is ok this way! -- Greetings, Pim http://www.molmod.com --- --- --- -

Re: [Jmol-developers] Fwd: JMol applets dying at random

Randy. I think what you really need is the DATA command because it allows you to then also add a callback letting you know the script completed. Using setTimeout just causes problems in this case. Sent from my iPhone On Mar 22, 2009, at 12:26 PM, Randy Zauhar wrote: Bob, I followed the

[Jmol-developers] Jmol 11.6.RC4 and refactoring

Jmol Developers, Jmol 11.6.RC4 has some substantial refactoring. Any testing you wish to do would be appreciated. All the symmetry-related aspects (space groups, point groups, unit cells) are now all in their own package. These methods are in a new jar file, JmolApplet0_Symmetry.jar. That file

Re: [Jmol-developers] popup menu workaround for Java 1.6/1.7 security

Jonathan Gutow wrote: >On Aug 7, 2008, at 12:13 PM, Bob Hanson wrote: > > > >>Forget it. Here's the deal. >> >>It turns out that an applet can pop up a "menu" that consists of an >>image covering the ENTIRE SCREEN. >>Or a set of "

Re: [Jmol-developers] popup menu workaround for Java 1.6/1.7 security

Rolf Huehne wrote: >Bob Hanson wrote: > > >>Forget it. Here's the deal. >> >>It turns out that an applet can pop up a "menu" that consists of an >>image covering the ENTIRE SCREEN. >>Or a set of "menus" that collectively cover

Re: [Jmol-developers] Another thought on the pop-up applet menu...

Jonathan Gutow wrote: >I think it would be possible to put the "menu bar" at the bottom of >the applet. I also think it could be made to only extend over the >region we currently use for the Jmol frank. Then the frank would >become a normal menu and right-click could activate that. I did a

Re: [Jmol-developers] popup menu workaround for Java 1.6/1.7 security

t;in it). This could then behave just like our pop up menu. I sort of >like the idea that it wouldn't go away completely without my deciding >to dispose of it. It then becomes like a combination pop-up and >palette. > >Jonathan >On Aug 6, 2008, at 7:26 PM, Bob Hanso

Re: [Jmol-developers] A place the calculate point group function doesn't work...

that. > Just a thought. > > Xavier > > On Wed, Aug 6, 2008 at 5:23 PM, Bob Hanson <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > I just uploaded a fix -- should be good as SourceForge. And Nico just > released a version, so please c

Re: [Jmol-developers] popup menu workaround for Java 1.6/1.7 security

Rolf Huehne wrote: >Bob Hanson wrote: > > >>I think I have a fix for the prospect that unsigned applets can no >>longer (or soon to be no longer) able to pop up a menu. My plan: >> >>1) Add a menu bar to the console. >>2) pop up the console on right-clic

[Jmol-developers] popup menu workaround for Java 1.6/1.7 security

I think I have a fix for the prospect that unsigned applets can no longer (or soon to be no longer) able to pop up a menu. My plan: 1) Add a menu bar to the console. 2) pop up the console on right-click of the mouse. A bonus is that we can then have a top-level help menu item that really provid

Re: [Jmol-developers] A place the calculate point group function doesn't work...

/index.php?molecule=92 > Hyponitrous Acid : CS : C1 > http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=98 > > Xavier > > > On Wed, Aug 6, 2008 at 2:28 PM, Jonathan Gutow <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > &g

Re: [Jmol-developers] A place the calculate point group function doesn't work...

1.4116 0. >CONECT1234 >CONECT21 >CONECT31 >CONECT41 >END >------ >On Aug 6, 2008, at 11:45 AM, Bob Hanson wrote: > > > >>Try the very lastest version at >>http://chemapps.stolaf.edu/jmol/docs/examples

[Jmol-developers] FYI - Sun Java bug in 1.6.0_10 beta

Bummer! Sun Java 1.6.0_10 beta (latest version, Build 25) appears to have a bug that disables the popup menu. Anybody know anything about this? -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what

Re: [Jmol-developers] A place the calculate point group function doesn't work...

Try the very lastest version at http://chemapps.stolaf.edu/jmol/docs/examples-11 working for me Jonathan Gutow wrote: >Bob, > Calculate PointGroup is coming along nicely. However, it is >identifying trigonal planar structures with identical species at the >trigonal positions a

Re: [Jmol-developers] Question about efficiency and java import operation...

It makes no difference. I do this periodically just to be more specific for myself as to what classes are really being accessed. Jonathan Gutow wrote: >I noticed that a bunch of "import ..*" lines were replaced >recently with specific imports of single classes. Does this make the >f

[Jmol-developers] [Fwd: SourceForge.net Project Web/Shell/Database Migration on 2008-08-18]

FYI Original Message Subject:SourceForge.net Project Web/Shell/Database Migration on 2008-08-18 Date: Wed, 6 Aug 2008 14:20:42 UT From: SourceForge.net Team <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Greetings, The date for the migration of the project web, da

Re: [Jmol-developers] There may be a problem with embedding scripts as comments in html/xhtml

Make sure the header does not indicate that this is XHTML. Jonathan Gutow wrote: >I was looking something else up and ran across the following in the >xhtml specifications: > >C.4. Embedded Style Sheets and Scripts > >Use external style sheets if your style sheet uses < or & or ]]> or >--.

Re: [Jmol-developers] location of toolbar button images

I was thinking of just a ruler with the letter D, A or T, but there's probably something better. If the three can have some common element (like the ruler) that would be fine. I haven't taken a look at your icons yet. Bob Angel Herráez wrote: >Bob Hanson wrote: > > &g

Re: [Jmol-developers] location of toolbar button images

Great! Angel, can we have three measurement icons, please -- Distance, Angle, and Torsion? Bob Angel Herráez wrote: >A recent post of Bob's in jmol-users has prompted me to change the >rotation button and some other icons in the application toolbar. > >Can anyone advise if the proper place to

Re: [Jmol-developers] I've found the 11_4 branch in the svn tree...do I put bug fixes there?

right -- you need to do those changes in both branches. There's a way you can do that automatically, but if it's simpler, just copy the files. DO NOT drag files. Jonathan Gutow wrote: >Bob, > I was having a problem with eclipse not accessing the whole svn >structure, but it is now fixed

Re: [Jmol-developers] Are we going to have a bugfix release for 11.4 soon?

trunk is 11.5, not 11.4. Can you just use 11.5? It's up. Jonathan Gutow wrote: >AS I am presenting a talk on the export to web function next week, >I'm sort of keen to have the bug fixes I recently submitted for >Export to Web in the current release version. When is the next >release? The

Re: [Jmol-developers] Do I need to maintain backwards compatibility of the JmolPopin.js code?

y for people editing the page to mess up the >javascript. Eventually, if JmolPopin.js settles completely we might >want to move it to be part of the standard Jmol installation, but >we're not ready yet. > >Jonathan > > >On Jul 21, 2008, at 6:25 PM, Bob H

Re: [Jmol-developers] Do I need to maintain backwards compatibility of the JmolPopin.js code?

e to start and then go in and edit the scripts to >do loops other things. Is it harder to do that to scripts included >in the .html file? > >Jonathan >On Jul 21, 2008, at 8:47 AM, Bob Hanson wrote: > > > >>right -- and, Jonathan, I'd like to show you how

Re: [Jmol-developers] Do I need to maintain backwards compatibility of the JmolPopin.js code?

; >Jonathan >On Jul 21, 2008, at 2:58 PM, Bob Hanson wrote: > > > >>It's really easy to edit the scripts. They look just like normal >>scripts, and they can be well marked. You can have any number of >>scripts >>in an HTML file because they are just

Re: [Jmol-developers] Do I need to maintain backwards compatibility of the JmolPopin.js code?

ipts to >do loops other things. Is it harder to do that to scripts included >in the .html file? > >Jonathan >On Jul 21, 2008, at 8:47 AM, Bob Hanson wrote: > > > >>right -- and, Jonathan, I'd like to show you how we can make the >>scripts >&g

Re: [Jmol-developers] measurements: 3 atoms reported in console instead of 2

That should be fixed for 11.5.49, now available in http://chemapps.stolaf.edu/jmol/docs/examples-11 This release also involves a compiler rewrite, so please be on the alert for commands misbehaving. My script testing (involving several thousand lines) showed no problems. Bob Angel Herráez wr

Re: [Jmol-developers] measurements: 3 atoms reported in console instead of 2

Thanks, Angel. That's fixed. Nico -- we should release 11.5.49. I'll post files at my site momentarily. Bob Angel Herráez wrote: >Jmol 11.5.47 >Not sure if this is significant, but I'm seeing a strange report in the >console when I make a >distance measurement using the mouse: rather than two

Re: [Jmol-developers] Do I need to maintain backwards compatibility of the JmolPopin.js code?

right -- and, Jonathan, I'd like to show you how we can make the scripts all part of ONE file -- the HTML -- so that there will be none of this multiple SPT file problem at all. Bob Jonathan Gutow wrote: >Dear all: > I've thought of a way of making the javascript for the export to web

Re: [Jmol-developers] Help request

John, I'm forwarding this to the Jmol developer list. People there know better than I. Primarily Eclipse, Java SDK, and lots of help from other developers. Bob John Penn wrote: > Bob, > What programs do I need to program the java, compile it, and then > deploy it? > > Any help that you ca

Re: [Jmol-developers] QueueThread problem

great -- that's in now for 11.5.48. Charles(Qian) Xie wrote: > Hi Bob: > > I found that destroy() cannot clear the memory leak problem in the > following scenario: > > If there are multiple Jmol windows in a page and some of them are not > visible until the > page is scrolled, the scripts sent

Re: [Jmol-developers] partial bonds: type 8 in MOL format, changes along versions, a bug?

I'll need some specific file examples, please. Angel Herráez wrote: >According to a previous report of mine (which went into doc. in the Wiki) >http://www.mail-archive.com/[EMAIL PROTECTED]/msg09232.html >in MOL format files, bond type 8 (described as "any") used to be interpreted >by Jmol as

Re: [Jmol-developers] Absolute URL in Jmol

just use the absolute url. Is there a problem with that? Jmol can use both. Alexandre MEJAT wrote: > Hi, > > I would like to include Jmol in eyeOS (www.eyeos.org > ) but I have a difficulty with the way Jmol > deals with URL. > > eyeOS reproduces a desktop like environment

Re: [Jmol-developers] Partial charges in XYZ format

cells, symmetry operations) to this file format simply by adding UNITCELL and SPACEGROUP parameters to the LOAD command. In other words, you can "retrofit" simple xyz data to an original full-symmetry format. That is really a very powerful capability of Jmol. Bob >Regards, Michael &g

Re: [Jmol-developers] Partial charges in XYZ format

OK, that's in for 11.5.41. For some reason the reader was set up to round that charge. I consider it a bug. Fixed also for 11.4.5. Bob Michael Sternberg wrote: >On Jun 16, 2008, at 10:28 , Michael Sternberg wrote: > > >>I like the XYZ format for its simplicity and >>flexibility in optionall

Re: [Jmol-developers] Internal Data Representation

command won't be queued like the original script command would be. If that turns out to be an issue, we can make Viewer.defineMeasurement(Vector monitorExpressions, float[] rangeMinMax, boolean isDelete, boolean isAllConnected, boolean isSho

Re: [Jmol-developers] Internal Data Representation

Brian, why not just do it with a simple Jmol script: measure ALL {*} {*}; show measurements Brian Ramos wrote: > Hi, > > (Since this is a different question, I figured I'd start a different > thread.) > > I'm trying to add a reporting feature that will calculate distances > between all pair

Re: [Jmol-developers] Highlighting Atoms

working on the 11.4 branch, is there > another way that I can get this done? > Would you suggest just porting my code to 11.5? > > Thanks, > Brian > > > On Fri, Jun 13, 2008 at 6:43 PM, Bob Hanson <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote:

Re: [Jmol-developers] Highlighting Atoms

1.5? > > Thanks, > Brian > > > On Fri, Jun 13, 2008 at 6:43 PM, Bob Hanson <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Brian, > > > This is done automatically using selectionHalos. You can set that so > that it toggle

Re: [Jmol-developers] Highlighting Atoms

Brian, This is done automatically using selectionHalos. You can set that so that it toggles on/off (selected/not selected) with each click using set selectionhalos on set picking select Great! Let us know if you have any more problems or just ideas for that implementation. Please be sure to u

[Jmol-developers] oops

Jmol developers: The current Jmol code at SourceForge is broken. It has to do with the unsigned applet. I was working on the signed applet --- that is fine --- but I forgot to check on the unsigned applet. The released 11.5.39 code is fine; it's just the very latest SVN code that is broken. I'l

Re: [Jmol-developers] Jmol/Protein Explorer development notes

Bob Hanson wrote: >Fellow Developers, > >Regarding using the signed applet and http://chemapps.stolaf.edu/pe/protexpl > > > >Heck, with a little server help, we should be able to have that site >EMAIL the Jmol state to yourself or a colleague as an attachment. OK, &g

Re: [Jmol-developers] Jmol/Protein Explorer development notes

this regard. Do the new browsers let you walk through the JavaScript, setting breakpoints and such? Anyone had any success with that? Bob Bob Hanson wrote: >Jmol developers: > >Take a look -- Protein Explorer now works with Jmol! > >http://chemapps.stolaf.edu/pe/pro

Re: [Jmol-developers] Uploading changed package to SourceForge

use RIGHT-click - menu team...|Synchronize This will show all files changed on both ends. Then ask for a commit to upload your files. Look out for red flags -- that means someone else has made changes. If that's the case, that's another lesson Bob Andrew R Turner wrote: >Hi All, > >I ha

[Jmol-developers] Jmol/Protein Explorer development notes

Jmol developers: Take a look -- Protein Explorer now works with Jmol! http://chemapps.stolaf.edu/pe/protexpl -- developer notes -- This uses the signed applet, and I'm happy to say it works extraordinarily well. There are going to be limitations -- serious thought, for example, should be giv

[Jmol-developers] A quiz for you / Protein Explorer - Jmol

Jmol Developers Exciting news. The Jmol/Protein Explorer implementation is coming along nicely. Take a look at http://chemapps.stolaf.edu/pe/protexpl and let me know what you think. This uses some very advanced techniques inside and outside of Jmol. So far I have all the basic stuff working, an

Re: [Jmol-developers] Using jmolSetCallback

sure -- »»»JIJI«««.: wrote: > Dear Bob Hanson, > > I didnt know how and were to use this code, in my page, can you tell > me briefly, > > I am sending my code below your code: > > > > //My code/// > > > > Jmol- Test >

Re: [Jmol-developers] (no subject)

SwingSet2 App Sun Microsystems, Inc. http://java.sun.com/products/javawebstart/demos.html"/> SwingSet2 Demo Description SwingSet2 Demo Short Description http://java.sun.com/products/autodl/j2se"/> B

Re: [Jmol-developers] Catch error in jmol

You can catch it with the message callback system. Something like this: function myfunc(app,message){ var s = message + "" // BE SURE TO DO THIS! if (s.indexOf("ERROR")>=0 && s.indexOf("load >>") >= 0) { jmolScript("zap") } } jmolSetCallback("messageCallback", "myfunc") the message is i

Re: [Jmol-developers] Creating bond between two models

»»»JIJI«««.: wrote: > Dear All, > > > I have two models 1PRG.PDB and 4HHB.PDB, > > My probelm is , i want to create bond between suppose , > > SER A 123 (1PRG) <=> PRO B 34 (4HHB) > > So how to give the command with atomno and chain to build bond > > You cannot make bonds between models. If y

Re: [Jmol-developers] Executing commands from the GUI

Andrew R Turner wrote: >Hi, > >Now that my teaching commitments are finished for the moment I have a >chance to get on with working on the dialogs in Jmol. I have had a >look around the code and I have a question: how do you execute a jmol >command using the GUI? > >I know how to create butt

Re: [Jmol-developers] jmolApplet0 inside div

In the jmolApplet call, don't use the full tag -- jmolApplet0 -- use just an extension, and don't use "0", because that might be misinterpreted by some browsers as 0. document.getElementById("datadiv").innerHTML = jmolApplet(500, jmoltext, "1"); then, in your call to jmolScript, refer to that

Re: [Jmol-developers] line missing when using jmolGetPropertyAsString("stateInfo") and getState()

This bug is fixed for Jmol 11.5.27. In the mean time, just make sure you add a space character to the beginning of any file data starting with \n or \r. Bob Angel Herráez wrote: >Sorry if that wasn't clear enough. > >I'm reading the state from the original window using > var x = jmolGet

Re: [Jmol-developers] minimization

Angel Herraez wrote: >Bob Hanson wrote: > > > >>that's next. I have an idea but no time to work on it. It would involve >>the MOL2 format bond stereochemistry designations. >> >> > >I can't find anything about stereochemistry in th

Re: [Jmol-developers] minimization

Angel Herráez wrote: >So I've being playing for a few days with the minimization of structures in >Jmol, and I'm very >happy with the result; I think it will make an excellent educational tool. I'm >feeding Jmol with >2D structures drawn and then exported into MOL format. >(All this runs with

[Jmol-developers] Jmol 11.5.23

version=11.5.23 # new feature: minimize ENERGY # no stepping # new feature: minimize STEPS n # new feature: minimize CRITERION x.y # new feature: minimize CLEAR # flushes logged info and saved atom info # # new feature: echoCallback # new feature: measureCallback # new feature: minimizationCallbac

Re: [Jmol-developers] Jmol 11.5.21 -- MINIMIZATION

Egon Willighagen wrote: >On Fri, Mar 28, 2008 at 8:07 PM, Bob Hanson <[EMAIL PROTECTED]> wrote: > > >> I had some very strange cross-SVN branch thing going on there. A few >> files in my checked out Trunk turned out to be in my branch, so I was >> committing c

Re: [Jmol-developers] IE-specific problem with jmolLoadInline()

Try it now. Angel Herráez wrote: > Thanks Bob, but... > > 1.- The link is mistyped, should have a hyphen rather than an underscore: > > http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.js > right, thanks. > > 2.- I am getting a javascript error in Firefox: > > Error: applet.loadInlineScript

Re: [Jmol-developers] IE-specific problem with jmolLoadInline()

This appears to be an Internet Explorer 7 bug -- arrays are not passed the same way as they were before to the applet. I've uploaded a Jmol.js fix for this at http://chemapps.stolaf.edu/jmol/docs/examples_11/Jmol.js and also http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/ap

Re: [Jmol-developers] Jmol 11.5.21 -- MINIMIZATION

It's a separate thread, so you can do odd things, like rotate the model while it is minimizing. --- or even set it spinning, I think! I'm thinking what we need is some sort of a minimization callback so that the user can get messages as the model updates. Then we also need to be setting variab

Re: [Jmol-developers] Jmol 11.5.21 -- MINIMIZATION

Angel, There problem was with the torsional calculation. I've uploaded a modified jar files. -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm That thyroxine.cml minimizes just fine now. Developers, I had some very strange cross-SVN branch thing going on there. A few files in

Re: [Jmol-developers] Jmol 11.5.21 -- MINIMIZATION

I'm guessing that the UFF forcefield is more tuned to getting energies right than structure. If that's the case, it may take some tweaking, and we may want to implement some alternative parameterizations that stiffen the structure (at the expense of energy). Or there could be a bug Bob An

Re: [Jmol-developers] Jmol 11.5.21 -- MINIMIZATION

try the jar file at http://chemapps.stolaf.edu/jmol/docs/examples-11 Angel Herráez wrote: >So I've tried the new minimization, but had hit a stone wall. >I downloaded 11.5.21 from SF (BTW, the popup says 2008-03-02) >Loaded a flat thyroxine molecule in CML format, and issued > >$ minimizationStep

Re: [Jmol-developers] Jmol 11.5.21 -- MINIMIZATION

hmm. Don't know. I've only tried it on a couple of files. What does the Java console say? Angel Herráez wrote: >So I've tried the new minimization, but had hit a stone wall. >I downloaded 11.5.21 from SF (BTW, the popup says 2008-03-02) >Loaded a flat thyroxine molecule in CML format, and issued

[Jmol-developers] Jmol 11.5.21 -- MINIMIZATION

Nico, you can release 11.5.21. All, I don't have time today to go over the details, because I'm running out of town in 5 minutes. Thanks to Tim Vandermeersch and Geoff Hutchison for their generous contribution to Jmol of a minimizer for the UFF force field. This added a new Jar file to the appl

Re: [Jmol-developers] Jmol and UFF

Egon, I'm worried I detect sarcasm in that message. Just asking for clarification. Bob Egon Willighagen wrote: > cc: cdk-devel > > On Sun, Mar 23, 2008 at 2:08 PM, Geoffrey Hutchison > <[EMAIL PROTECTED]> wrote: > >> On Mar 23, 2008, at 2:16 AM, Egon Willighagen wrote: >> > Unless this wou

Re: [Jmol-developers] Jmol and UFF

Tim, Geoff, and Jmol Developers. Thanks to Tim and Geoff for some great pointers, I have a branch of Jmol close to doing UFF minimizations. I've seen it "fix" a distorted caffeine structure, but I'm not claiming success yet. Just indicating that: *The C++ to Java port of the OpenBabel code is

Re: [Jmol-developers] Getting started with Jmol development

you need help, just ask. At one point or another I'll merge back from your branch to the root to incorporate your contributions. That sound OK? Happy coding! Bob Andrew Turner wrote: >Sorry, forgot to include it! It is 'atrog'. > >Andy > >Bob Hanson wrote: >

[Jmol-developers] 11.5.17 - new DELETE command

Nico, 11.5.17 is ready for release. It includes the capability to delete specific atoms. These atoms are not actually removed from memory -- use ZAP for that -- but instead for all practical purposes deleted. (We could always UNDELETE them, if we had that command.) Not 100% sure this is compati

Re: [Jmol-developers] Jmol 11.5.16 - atom deletion using ZAP

Correction. In 11.5.16, in fact, dots weren't zapped properly. Also, for that version you have to specify full models using the file.model notation, not just subsets of the models. This is corrected for 11.5.17. Bob Bob Hanson wrote: > Jmol Developers, > > I have uploaded Jmol 1

[Jmol-developers] Jmol 11.5.16 - atom deletion using ZAP

Jmol Developers, I have uploaded Jmol 11.5.16 -- Nico, please release 11.5.16 and 11.4.0 The big new thing is the ability to delete individual models. You do this by selecting ATOMS, and then Jmol deletes all models involving the selected atoms. For example: load files "caffeine.xyz" "1crn.pd

Re: [Jmol-developers] Getting started with Jmol development

what's your SourceForge user name? Andrew Turner wrote: >Hi Bob, > >OK. Give me a branch and I will see what I can come up with. > >Cheers > >Andy > >Bob Hanson wrote: > > >>Andrew Turner wrote: >> >> >> >>>Hi >>&

Re: [Jmol-developers] New export formats

Andrew Turner wrote: >Bob > >I have renamed the thread to something more relevant. > > > >>Be sure to take a look at the >> >> write COORDS >> >>command. With it you can export PDB, XYZ, or MOL file data. The files >>are based on whatever atoms are currently selected. Is this perhaps all >>you

[Jmol-developers] atom deletion?

licates and rotateSelected Date: Tue, 11 Mar 2008 20:28:46 -0500 From: Bob Hanson <[EMAIL PROTECTED]> Reply-To: [EMAIL PROTECTED] To: [EMAIL PROTECTED] References: <[EMAIL PROTECTED]> He wants his duplicates and to eat them, too! I don't know Delete atoms

Re: [Jmol-developers] Getting started with Jmol development

w when you want to get started, and I will create a branch for you and enable your access as a developer if you don't have it already. Sounds wonderful. Bob >Regards > >Andy > > > >Bob Hanson wrote: > > >>Andy, welcome aboard! Tell us about yours

Re: [Jmol-developers] Getting started with Jmol development

Andrew Turner wrote: >Jonathon, > >I know and use some of those programs and I am not proposing that Jmol >should have a builder section. All I am talking about developing is >dialogs that can save the currently viewed molecule (wherever that came >from) as an input file for the codes I mention

Re: [Jmol-developers] JMOL and molecular lipohilic(ity) potential - some hints how to calculate

OK, that's a great start, Reinhold. Now I need a volunteer to make this their legacy contribution to Jmol. Any takers? Reinhold Stoermann wrote: > A few weeks ago I asked you about the possibility to show "molecular > lipohilic(ity) potential" (MLP) with jmol, as can be done with Chime. > > Yo

Re: [Jmol-developers] Getting started with Jmol development

Andy, welcome aboard! Tell us about yourself. I'm probably the only one right now who really knows everything that is in the code and how it works. So ask me anything. One thing you can look at is the viewer.gif file in http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/_docume

Re: [Jmol-developers] model interaction

Actually, the easiest way is to use JmolViewer.getProperty(null, "chainInfo", "") This returns a HashTable with entry "models" that is a Vector. Each models element is a HashTable with entry "chains", which is a Vector. Each chains element is a Hashtable "residues", which is a Vector of the gr

Re: [Jmol-developers] model interaction

Charles Musgui wrote: > Hello, > > I would like to know how I can interact with a protein model loaded > within JMol. To be more precise, here is what I'd like to do, directly > using the JMol API: > 1. get the protein model, then get the Chain IDs contained in the > model (I suppose here I han

Re: [Jmol-developers] Jmol attends "Molecular Modelling: Tools, GUIs and Visualisation"

Wow - very nice, Angel! Additional capabilities you may want to mention: -- atoms can be added (DATA "append") -- save/restore of exact state of the model -- export also to Maya and VRML -- export is completely user-customizable, based on a Java interface: Drop in a new exporter java module you

Re: [Jmol-developers] IMPORTANT (NOT SPAM): SF pwd expired

thanks, Egon. That explains my experience! Egon Willighagen wrote: >Hi all, > >I just had trouble committing to SVN, and it likely has to do with >this message from SF: > >"( 2008-03-06 14:23:47 - SourceForge.net Web Site ) In support of >improved security, all SourceForge.net user passwords

Re: [Jmol-developers] selecting Atoms/Residue/Molecule from applet

»»»JIJI«««.: wrote: > Dear ALL, > > Is their is any way to get the Atoms/Residue/Molecule from the applet > which the user select > > > The atom index (0 through N) of the atom picked is saved in the _atomPicked variable. You can use a pick callback and then something like: var group =

Re: [Jmol-developers] Cannot call JSObject.call() from StatusManager.java

oooh, please don't do that! All JavaScript calling should be taken care of in Jmol.java, within the MyStatusListener interface. I recently made jsoWindow a local there because it is unreliable as a long-term variable. (The page may close.) If you want to call a JS function, can you use the Jav

Re: [Jmol-developers] Jmol attends "Molecular Modelling: Tools, GUIs and Visualisation"

Great! Thanks for doing this, Angel. Angel Herraez wrote: >Dear developers: > >I'd like to let you know that next week I will be participating --as >a Jmol representative ;-) -- in >"Molecular Modelling: Tools, GUIs and Visualisation" >a CCP1 meeting looking at graphical interfaces, >visualisa

Re: [Jmol-developers] Molecular Orbitals from Gaussian output

Xavier-- I checked all the files you provided on that web site, and the orbitals look terrific now. By the way, I note that the following script commands could be quite useful: print getProperty("auxiliaryInfo", "models", 2, "modata","mos") energy-20.2 coefficientsfloat[7] array

Re: [Jmol-developers] Molecular Orbitals from Gaussian output

users will have to specify 5D in the Gaussian > input. The calculation will contain just a bit smaller basis set in > comparison > with the default one, but at least it can be read by jmol: > I tested this in the previous examples, and now it works!! > http://144.92.39.89/xavier/mo/5d

Re: [Jmol-developers] Molecular Orbitals from Gaussian output

OK, I found it. It is a bug. Introduced when we added spherical (5D) sets. The 7F functions present here fool Jmol into thinking that these are spherical sets. So when we added F orbitals, we didn't realize that the 7F might be combined with a 6D instead of a 5D. I can fix this Thank you eve

Re: [Jmol-developers] Molecular Orbitals from Gaussian output

OK, I'm pretty sure this is not a bug. First, I note that the STO-3G orbitals are just fine. (right?) Here's your problem, I think, with the 6-31G(d) set: There are 4 symmetry adapted basis functions of A1 symmetry. There are 0 symmetry adapted basis functions of A2 symmetry. There

Re: [Jmol-developers] Molecular Orbitals from Gaussian output

Very much appreciate your finding that, Xavier. We did a lot of testing of that, but it's still possible that there is a bug there. I will definitely look into it immediately. By the way, you can deliver those cube files as JVXL format surfaces with very little files space if you want to. http:

  1   2   3   4   5   6   7   8   9   10   >