[Jmol-users] SMOL Files

, that can export Jmol readable files with electrostatic data for MEPS display? Otis Rothenberger [EMAIL PROTECTED] - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event

Re: [Jmol-users] SMOL Files

the file to me. Bob Hanson Otis Rothenberger wrote: Hello- I'm interested in taking a closer look at using Jmol to display MEPS. The Jmol sample smol files for benzene and fluoromethane work very nicely. The smol file type appears to be a Spartan related file type. I'm having trouble

[Jmol-users] UFF Feature

. You must be explicit with hydrogen atoms. Getting a six member ring to chair rather than boat takes some JME drawing care, but being able to get either a chair or a boat into Jmol is pretty neat. To repeat myself, wonderful addition! Otis -- Otis Rothenberger http://chemagic.org

[Jmol-users] Wedge Bonds and Model Load Flag

? At the risk of repeating myself too often, the UFF addition to Jmol simply delightful. Thanks again to the developers responsible for including this. Best Regards, Otis -- Otis Rothenberger http://chemagic.org -- Return

Re: [Jmol-users] Wedge Bonds and Model Load Flag

On Tue, Dec 8, 2009 at 12:43 PM, Otis Rothenberger o...@chemagic.com wrote: Hello Angel- The page in question is: http://chemagic.com/web_molecules/script_page_large.aspx The draw structure link on the page is the operative link. I've attached a png file of the screen at the point where

Re: [Jmol-users] Wedge Bonds and Model Load Flag

://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger http://chemagic.org -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev

Re: [Jmol-users] Wedge Bonds and Model Load Flag

- ChemSketch. The upside is that ChemSketch Free is a tool that organic students should have on their computers. Otis -- Otis Rothenberger http://chemagic.org -- Return on Information: Google Enterprise Search pays you

Re: [Jmol-users] Wedge Bonds and Model Load Flag

. -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis

[Jmol-users] Mouse Move Detection

back, but is there any way to pick up a move into the applet or a click on any part of the applet - i.e. bonds, atoms, or background? Otis -- Otis Rothenberger http://chemagic.org -- Return on Information: Google

Re: [Jmol-users] Mouse Move Detection

() } somewhere after the applet has been inserted (e.g. at the end of the body). And it does work! The first time it seems to take some delay, though. The test function is defined elsewhere and does whatever you want. -- Otis Rothenberger http://chemagic.org

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

() {) -1) { jmolVar1 = messageString + ; } } Put state info in new Jmol applet: function pasteMol() { if (feedbackFlag) { feedback(r[9]); } // Relevant to my page only. evalRasmol(select *); evalRasmol(jmolVar1); } Best Regards Otis -- Otis Rothenberger http://chemagic.org

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

, at 8:16 AM, jmol-users-requ...@lists.sourceforge.net wrote: Date: Fri, 18 Dec 2009 08:16:32 -0600 From: Otis Rothenberger o...@chemagic.com Subject: Re: [Jmol-users] Need help passing a state script form one       applet  to another via javascript... To: jmol-users@lists.sourceforge.net Message

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

, false); Convoluted! But I think this answers part of your question. Best, Otis -- Otis Rothenberger http://chemagic.org -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's

Re: [Jmol-users] Jmol demo page hangs

); Ignoring my load script, jmeString is simply the un-doctored coordinate string (molfile) from JME - i.e. no concatenated LF or CR/LF. Otis -- Otis Rothenberger http://chemagic.org On Wed, Jan 13, 2010 at 1:12 PM, Grossman, Robert B robert.gross...@uky.edu wrote: Hi, I'm trying to figure out how

Re: [Jmol-users] Jmol usually not displaying molecule

responds to this page. I hope the above information is of some use to you. As an aside, check out Jmol's UFF fuction on your model once (if?) it loads (UFF link). I think this relatively new addition to Jmol is really neat. Otis -- Otis Rothenberger http://chemagic.org

Re: [Jmol-users] Jmol usually not displaying molecule

quotes (#39;). Is that the intent? I'm using Jmol 11.9.9. Otis -- Otis Rothenberger http://chemagic.org -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field

Re: [Jmol-users] Marvin Sketch

/jmol-users -- Otis Rothenberger http://chemagic.org -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees

Re: [Jmol-users] Marvin Sketch

followed by Clicking the UFF link gets the job done for the Marvin Beans structure in the text field. Otis On Fri, Jan 15, 2010 at 8:01 PM, Otis Rothenberger o...@chemagic.com wrote: Bob, I have a page that does this with the JME drawing applet. I'm not sure if this will help: http

Re: [Jmol-users] Marvin Sketch

, and it should have your calculate hydogens or minimize addHydrogens On Sat, Jan 16, 2010 at 12:35 AM, Otis Rothenberger o...@chemagic.com wrote: I should mention that the page also has a ChemSketch link. This link simply does an inline molfile load of a molfile pasted in the page's text field

Re: [Jmol-users] Marvin Sketch

, Robert Hanson hans...@stolaf.edu wrote: OK, so Nico has released 11.9.19, and it should have your calculate hydogens or minimize addHydrogens On Sat, Jan 16, 2010 at 12:35 AM, Otis Rothenberger o...@chemagic.com wrote: I should mention that the page also has a ChemSketch link

[Jmol-users] Coincident Hydrogens with minimize addHydrogens

, but these two general cases quickly caught my attention. It probably goes without saying, but allene and ketene produce the same result. Otis -- Otis Rothenberger http://chemagic.org -- Throughout its 18-year history

[Jmol-users] MEP Display

). What is the current recommendation for a MEP script? Again, the partial charges in the files are reasonable, and they can be read by a direct call to: select; wireframe 0.03; spacefill 1%; spacefill 1%;label \%-8.3[partialcharge]\; Otis -- Otis Rothenberger http://chemagic.org

Re: [Jmol-users] MEP Display

. If you find a set that is a better default, we could consider that for Jmol 12, which I think is probably on the horizon. Bob On Sun, Jan 24, 2010 at 11:46 AM, Otis Rothenberger o...@chemagic.com wrote: Hello- 1) I thought range all was default, but there must be another default. What

Re: [Jmol-users] MEP Display

) More like the Jmol default. I expected that this would be the same as A - i.e. min to max = all Again, a point of information: Snip B) with -0.05 +0.05 essentially produces the Jmol menu MEP for both Spartan data and Accelrys data. Otis -- Otis Rothenberger http://chemagic.org

Re: [Jmol-users] Configuration Inversion

} @theAxis @theAngle select within(BRANCH, {C}, {Cb}) rotateSelected MOLECULAR {C} @theAxis @{-theAngle} Should do the trick. Bob On Tue, Feb 2, 2010 at 10:36 AM, Otis Rothenberger o...@chemagic.com wrote: Hello- I'm trying to invert the configuration of a single carbon atom

Re: [Jmol-users] Configuration Inversion

Bob- Absolutely NOT more than I wanted to know. Thanks for the tutorial. Otis Probably more than you wanted to know. Bob -- Otis Rothenberger http://chemagic.org -- The Planet: dedicated and managed

Re: [Jmol-users] Atom Replacement Problem

___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers

Re: [Jmol-users] calculate hydrogens + minimize locks Jmol 11.9.28

/jmol-users -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu

Re: [Jmol-users] Atom Replacement Problem

@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award

[Jmol-users] addHydrogens Problem

hydrogen atoms, but they are exactly superimposed in the molfile. A similar problem exists with a primary amine, but the hydrogens are offset slightly in this case. Subsequent minimization eventually gets them apart. Not so with the superimposed hydrogens on the alkene. Otis -- Otis Rothenberger

[Jmol-users] delete hydrogens minimize addHydrogens

to get high school chemistry students (and teachers) excited about using Jmol, and a working model page continues to attract attention. Obviously, true fixes are better than kludges, but that will take time. Otis -- Otis Rothenberger http://chemagic.org attachment: jmolPic.jpg

Re: [Jmol-users] delete hydrogens minimize addHydrogens

specific examples. I need to make sure that I have the most recent Jmol version. Is this still the 11.9.30_dev link that you sent in a previous email? Otis -- Otis Rothenberger http://chemagic.org -- SOLARIS 10

Re: [Jmol-users] delete hydrogens minimize addHydrogens

. Finally, you are correct delete by atomIndex does work. I'm not sure why I had a problem with this. Otis -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace

Re: [Jmol-users] delete hydrogens minimize addHydrogens

not work with cumulenes. Bob On Sun, Feb 14, 2010 at 2:56 PM, Otis Rothenberger o...@chemagic.comwrote: Bob, I think I have the latest version of 11.9.30_dev on the chemagic server: http://chemagic.com/web_molecules/script_page_large.aspx User instructions are sparse right now, but I think

Re: [Jmol-users] delete hydrogens minimize addHydrogens

oops, make that allene - not ketene A question on timing: Is there a way to prevent Jmol from accepting a JavaScript call to appletObject.script(string) until a running Jmol script is finished? Otis On Mon, Feb 15, 2010 at 12:25 PM, Otis Rothenberger o...@chemagic.comwrote: Bob, Your

Re: [Jmol-users] delete hydrogens minimize addHydrogens

. Actually, a separate minimize link makes sense for another reason. The minimize delay is really disruptive during model building. Otis -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers

Re: [Jmol-users] delete hydrogens minimize addHydrogens

atomInfo[11].formalCharge0 -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http

Re: [Jmol-users] delete hydrogens minimize addHydrogens

that my .js pages have become and then put the page on the chemagic server. Otis -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing

[Jmol-users] Get an Atom Property by Index

tried various string expressions (e.g. atomInfo['atomIndex=1'].color) for the index value, but I'm not having any luck. Otis -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers - provides

Re: [Jmol-users] Get an Atom Property by Index

number. It's just atomIndex + 1. (Because [0] means last element in this scripting language.) But just about all of these are now much more efficiently retrieved using, for example: jmolEvaluate({atomindex=1}.color) On Tue, Feb 16, 2010 at 8:54 PM, Otis Rothenberger o...@chemagic.comwrote

Re: [Jmol-users] Get an Atom Property by Index

:18 AM, Robert Hanson hans...@stolaf.edu wrote: On Wed, Feb 17, 2010 at 9:03 AM, Otis Rothenberger o...@chemagic.comwrote: Bob- I guess that I need to change to jmol.js, but doing so is going to bring down my house of cards! No, no. Not at all. You can do anything you are doing now

[Jmol-users] Help with Jmol Math

molecule size would be useful. One possibility is using math with zoom 100 and the orbit coordinates, 50 50 50. Is this math doable with zoom? Is there another math approach that can be used to redefine zoom 100? Any help with the above questions would be appreciated. Otis -- Otis Rothenberger http

Re: [Jmol-users] Help with Jmol Math

if the appended carbon atom is still being viewed with astatine's radius. That might explain the web of strange bonds. Whatever the situation, I have some direction now. Thanks for the help. Otis -- Otis Rothenberger http://chemagic.org

Re: [Jmol-users] Help with Jmol Math

].color[xff] atomInfo[8].infoH16 #16 atomInfo[8].atomIndex15 atomInfo[8]._ipt15 atomInfo[8].formalCharge0 -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try

Re: [Jmol-users] Help with Jmol Math

your other approach yet because I think it just sunk in as I read you last note. Did you mean select{*). add the carbon atom code here select unselected ??? Otis On Fri, Feb 19, 2010 at 2:37 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: Otis Rothenberger schrieb: Subsequent methylamine

[Jmol-users] Molecular Editor Questions

can reconnect the two fragments any way I want. I can also make two separate molecules of ethane. It appears that breaking off the following groups from a larger molecule creates the problem described above: CH3 OH NH2 SH Any suggestions? Otis -- Otis Rothenberger http://chemagic.org

[Jmol-users] Another Molecular Editor Question

of the substructure. -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel

Re: [Jmol-users] Molecular Editor Questions

sortOutOtisConvolutedWayOfDoingThings() for the replacement. :) I guess I'll just use processJmol(). Actually, the function processes Jmol and JavaScipt entered in the page's text field. Otis -- Otis Rothenberger http://chemagic.org

Re: [Jmol-users] Molecular Editor Questions

, Otis Rothenberger o...@chemagic.comwrote: Bob- Using your approach, picking deletes an H on propane. But minimize addHydrogens does not add it back. I'm thinking maybe I have the wrong Jmol version. I'm using 11.9.30_dev 2010-02-12 12:26. Is this the wong version? The two minimization steps

Re: [Jmol-users] Another Molecular Editor Question

logical attaching position of the substructure. -- Otis Rothenberger http://chemagic.org -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself

[Jmol-users] MSIE and Jmol bind

have any Mac information on this at this point. Otis -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively

Re: [Jmol-users] MSIE and Jmol bind

or unbound. Maybe MSIE 8 uses CTRL-LEFT for something else and doesn't pass it on the the applet. It should call up the menu. On Tue, Mar 2, 2010 at 8:49 PM, Otis Rothenberger o...@chemagic.comwrote: Hello- I'm using the bind command on Jmol 11.9.30_dev to set up mouse rotation

[Jmol-users] Mac Question re unbind/bind

this: http://chemagic.com/web_molecules/script_page_large.aspx Otis -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs

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

@{180.0 * _deltaY / _Height * mouseDragFactor}; rotate Y @{180.0 * _deltaX / _Width * mouseDragFactor}; But, right, there must be something about CTRL-LEFT and the Mac. Bob On Thu, Mar 4, 2010 at 12:30 PM, Otis Rothenberger o...@chemagic.comwrote: Hello, I'm using the following start up script

Re: [Jmol-users] MSIE and Jmol bind

...@stolaf.edu wrote: where's the page? On Tue, Mar 2, 2010 at 11:50 PM, Otis Rothenberger o...@chemagic.comwrote: Bob, Here is what's not working for me: jmolApplet(450, load /models/alkane!ethane_mm.mol;moveto 0 1 1 1 66;hover off;frank off;set PickCallBack 'processPick';javascript

[Jmol-users] Mac Java Configuration

have a feeling that he has some Java configuration, and possibly version problems. I understand that this is a very general question, but can anyone point me (him) toward recommendations for maximizing Mac/Jmol performance - Safari and Firefox. Otis -- Otis Rothenberger http://chemagic.org

[Jmol-users] Bind Unbind

a +/- wheel feedback handle like _DELTAX and _DELTAY for mouse feedback. I can bind the wheel, but movement along the Z axis is only +. Is there any wheeled forward/backward feedback information associated with BIND? Otis -- Otis Rothenberger http://chemagic.org

Re: [Jmol-users] Bind Unbind

that that out so you can try it. Question: Is there some reason we would see ** somewhere in select phrases rather than *? I'm pretty sure not. Bob On Thu, Mar 11, 2010 at 3:20 PM, Otis Rothenberger o...@chemagic.comwrote: I am using bind/unbind to move selected molecular fragments

[Jmol-users] Molecular Editor Problem

is set to do the with-hydrogen edit (works). If you do a delete hydrogens in the text command field, you will see the problem on the first C add. Any thoughts on the problem? It appears for the first click atomIndex=i is not what I think it is?? Otis -- Otis Rothenberger http://chemagic.org

Re: [Jmol-users] Molecular Editor Problem

a flash var pt = a.xyz * 2 - {connected(a)}.xyz set appendNew false; var w = '1\ntest\nC ' + pt.x + ' ' + pt.y + ' ' + pt.z + '\n'; data 'append @w'; var b = {*}[0] connect @a @b single; On Mon, Mar 22, 2010 at 11:29 PM, Otis Rothenberger o...@chemagic.comwrote: Bob, I am having an atom

Re: [Jmol-users] Molecular Editor Problem

the groups already present invert chirality completely. -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively

Re: [Jmol-users] Molecular Editor Problem

of this process, so I'd like to understand the problem. Otis On Fri, Mar 26, 2010 at 6:43 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 03/26/2010 06:30 AM, Otis Rothenberger wrote: Bob, I'm making some progress on your suggestion to check and branch during the addition of atoms (below

[Jmol-users] Load in Line Question

rather than that ridiculous atomIndex=1000, but that's not the problem here. -- Otis Rothenberger http://chemagic.org -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find

Re: [Jmol-users] Load in Line Question

Thanks Bob. That works nicely. Otis On Sat, Mar 27, 2010 at 10:15 PM, Robert Hanson hans...@stolaf.edu wrote: Ah, interesting! OK, that's fixed for Jmol 11.8.23 and 11.9.37 http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip -- Otis Rothenberger http://chemagic.org

[Jmol-users] State Save

of the code is that embedded molfile data rather than a server file load is intended to run. Am I correct on this assumption? If so, any thoughts on this problem? Otis -- Otis Rothenberger http://chemagic.org -- Download Intel#174

[Jmol-users] Jmol Virtual Model Kit

on this project, the url is: http://chemagic.com/web_molecules/ There is a users manual, but it's really in its early stages. I also linked the page to a video that gives a 3+ minute synopsis feel for how the application works. Any suggestions would be appreciated. Otis -- Otis Rothenberger

Re: [Jmol-users] Jmol Virtual Model Kit

is displayed. Drawing the cis-isomer loads the same Jmol display. If I use the X button of the editor to force hydrogens in the right configuration a nonsense structure is loaded. I am running Mac OS 10.4 Bill -- Otis Rothenberger chemagic.com

Re: [Jmol-users] Jmol Virtual Model Kit

with this note and post his reply. Otis On 4/9/2010 12:59 PM, r...@ellerbach.com wrote: On Fri, April 9, 2010 12:16 pm, Otis Rothenberger wrote: Downside: It's a helper application. Upside: ACD generously makes ChemSketch a free download for private, student, educational use. Isn't ChemSketch

Re: [Jmol-users] Jmol Virtual Model Kit

mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself

Re: [Jmol-users] Jmol Virtual Model Kit

on the model. Otis On 4/9/2010 1:07 PM, william reusch wrote: Otis, Are you transferring the JME structure as a Smiles string or as a JME string. The latter has more information in it. Bill Otis Rothenberger wrote: Bill, Thanks for the comments. The 2D to 3D translation

Re: [Jmol-users] Jmol Virtual Model Kit

- not linear. The addition of a set of cyclic hydrocarbon templates would be good. Otis On 4/9/2010 12:16 PM, Otis Rothenberger wrote: Bill, Thanks for the comments. The 2D to 3D translation is an ongoing problem for us. The JME editor is light weight and it can be embedded directly

Re: [Jmol-users] Jmol Virtual Model Kit

adding stereochemical reading, and it seems to work OK, but there is still a problem with the addhydrogens business. WIll fix On Fri, Apr 9, 2010 at 1:28 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Bill, I'm passing molfiles

Re: [Jmol-users] Jmol Virtual Model Kit

started to do this, I realize that the JME reader is totally nonfunctional. I'm adding stereochemical reading, and it seems to work OK, but there is still a problem with the addhydrogens business. WIll fix On Fri, Apr 9, 2010 at 1:28 PM, Otis Rothenberger osrot

Re: [Jmol-users] Jmol Virtual Model Kit and JME

___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new

Re: [Jmol-users] [ jmol-Feature Requests-2985130 ] Display of charges

, and it will display formal charge. 3. You could also color by charge, use ionic radii, ... See 1. http://wiki.jmol.org/index.php/File_formats/Coordinates [serach for charge in there] 2. http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#label -- Otis Rothenberger chemagic.com

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

then display. Question: does JME allow direct file reading, or it is only reading strings of data? If the latter, well, now it reads files. Bob -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

. JME.readMolecule(jmolEvaluate('load(' + filename + ')')) Bob On Mon, Apr 12, 2010 at 11:01 AM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Bob, I think it only reads strings. Implied in your note is the use of the following JME function via Live

[Jmol-users] Atom Info Problem Jmol 12.0.RC5_dev

check: alert(jmolGetPropertyAsString(moleculeInfo[1], all, 01)) shows correctly adjusted atomInfo. If, however, the substituted atom is univalent ( e.g. Cl vs C above), then the atomInfo formula remains unchanged - i.e. the ethane formula in the above example. Bug? Otis -- Otis

[Jmol-users] Jmol and JME 2D to 3D and 3D to 2D

-- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why

Re: [Jmol-users] Jmol and JME 2D to 3D and 3D to 2D

in this case. I realize this optimization could go on forever. I'd like to get it to a reasonable point for simple implementations for now. So send me JME strings of cases that don't work properly, and I'll see what I can do. But no promises. Bob Otis Rothenberger chemagic.com

Re: [Jmol-users] Jmol and JME 2D to 3D and 3D to 2D

in this case. I realize this optimization could go on forever. I'd like to get it to a reasonable point for simple implementations for now. So send me JME strings of cases that don't work properly, and I'll see what I can do. But no promises. Bob -- Otis Rothenberger chemagic.com

Re: [Jmol-users] Jmol and JME 2D to 3D and 3D to 2D

, you can only cycle between bold and hash in one direction. http://www.molinspiration.com/cgi-bin/properties On Apr 13, 2010, at 2:44 PM, Otis Rothenberger wrote: Bob, I'll put the new version on our server later today. I have to remove some JME load filters that I have on the page so

Re: [Jmol-users] Jmol and JME 2D to 3D and 3D to 2D

-- Otis Rothenberger chemagic.com http://chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune

Re: [Jmol-users] Jmol and JME 2D to 3D and 3D to 2D

to the limit. Otis On 4/13/2010 4:36 PM, Philip Bays wrote: I wrote to him yesterday, and I got the 2004 version, which I already had. Phil On Apr 13, 2010, at 3:20 PM, Otis Rothenberger wrote: I'm using a version that Peter sent to Tom in 2005. I just wrote to him to get the latest

Re: [Jmol-users] Jmol and JME 2D to 3D and 3D to 2D

-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling

[Jmol-users] JME Stereo Bonds

-methylpentane, at least on my system. Otis -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune

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

___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel

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

during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com

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

. Greencastle, IN 46135 jhan...@depauw.edu mailto:jhan...@depauw.edu *** -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new software tools

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

I'm sorry. That should be CTRL-LEFT, as per the code. I have to remember to check which hand has the scar! Otis On 4/15/2010 8:19 AM, Otis Rothenberger wrote: Jeff and Jonathan- Here's a Mac fix, I hope! First, I forgot. There is a WHEEL direction feedback. That allows this to be a bit

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

*** On Apr 15, 2010, at 1:01 AM, Otis Rothenberger wrote: Jeff and Jonathan- A single click on a bond would be nice, but I think only atoms (and possibly draw objects???) can pass to a clickcallback. This is very tentative, so I put it on the department server

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

*** -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel

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

. I think the WHEEL gives best control for bond rotation, but hopefully, item 3 covers a wheeless mouse. http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx Otis -- Otis Rothenberger chemagic.com

Re: [Jmol-users] JME Stereo Bonds

just click it in my opinion. Bob On Wed, Apr 14, 2010 at 11:20 AM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Ok, with a little help from Peter Ertl, I think I understand the JME's 4 stereo bond rotation. Maybe this was all resolved on the group

[Jmol-users] model to variable question

that model, can I put its molfile into a Jmol variable? Otis -- Otis Rothenberger chemagic.com -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs

Re: [Jmol-users] model to variable question

Bob, Thanks. This is the one I wanted: On 4/18/2010 10:09 PM, Robert Hanson wrote: If it is just a mol file, you can use within Jmol: var jmolx = getProperty(extractModel) Otis -- Otis Rothenberger chemagic.com

[Jmol-users] MO display problem

) on the following page will illustrate the problem: http://chemagic.com/web_molecules/script_page_large.aspx Has anyone else seen this problem? I don't think it is related to other code on the page. Otis -- Otis Rothenberger chemagic.com

Re: [Jmol-users] what is the reverse operation of jmolLoadInline?

-users@lists.sourceforge.net Subject: Re: [Jmol-users] what is the reverse operation of jmolLoadInline? Hello, Francois -- Otis Rothenberger chemagic.com -- ___ Jmol-users

Re: [Jmol-users] MO display problem

...@lists.sourceforge.net wrote: -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol

Re: [Jmol-users] MO display problem

OK, I see that this is fixed in RC7. I need to start checking updates more frequently! Otis On 4/21/2010 7:29 PM, Otis Rothenberger wrote: Thanks Jonathan, Yes, I am using 12.0.RC6_dev. I did not know about the approach: isosurface modelmo mo 1 I can make what I want to do work

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