Re: [Jmol-users] color temperature, translucent 'back end'

Frieda Reichsman wrote: > Hi, > > 1. For "color temperature", is it possible to specify a ROYGBIV > coloring scheme (or VIBGYOR) in place of the standard blue-white-red? > no. > 2. Any chance of implementing the following feature request - having > regions of the structure that are furthest fro

Re: [Jmol-users] [Jmol-commits] SF.net SVN: jmol: [8116] trunk/Jmol-FAH/projects

Congratulations to [EMAIL PROTECTED] for making it into the latest edition of PC Magazine! "Reinvent your PC -- 15 great uses for an older PC" by John Delaney #2: "Join the Distributed Computing Movement" PC Magazine September 4, 2007, page 56 "Become part of a worldwide network by joining a dist

[Jmol-users] lcaocartoon orbitals -- new feature "rotate"

Just checked in: 11.3.11 will include: lcaoCartoon rotate [x|y|z] [number_of_degrees] create "px" This allows a more precise positioning of LCAO cartoons. The axes are defined automatically by Jmol based on the local molecular structure around the specified center(s) and will be different for

Re: [Jmol-users] lcaocartoon orbitals

William Reusch wrote: >Jmol Gurus (probably Bob) > >I have encountered a glitch in the lcaocartoon method for drawing hybrid >orbitals. When a sp-hybrid carbon is bonded to a sp2-hybrid carbon the >create "sp" or "-sp" command fails to draw the hybrid orbitals. The >hybrid orbitals of the sp2

[Jmol-users] Jmol 11.3.10 released

Jmol 11.3.10 adds some interesting features and fixes a few bugs. Thanks, Nico, for that release. bug fixes - # bug fix: dots nn% not operational # bug fix: molecular dipole in multiple frame environment (note: you still only get ONE molecular dipole, no matter how many models you hav

Re: [Jmol-users] making movies

One other thing -- I just added to 11.3.10 the ability to adjust the JPG quality. The JPG file creator allows for an integer quality (1-100) parameter, and now we can pass that on. I think this would make movies from JPG sequences more managable -- when a subject is moving you don't need as hig

Re: [Jmol-users] making movies

rn-x2.wmv, which is a different server. Bob Hanson wrote: >Benny, > >The only reliable way I know of to do this is to set up a script and >have it dump images to a set of JPG files, then consolidate them into a >movie. Something like the following. I'm just setting the backg

Re: [Jmol-users] making movies

mportant (but a bug, I think). load =1crn; # http://chemapps.stolaf.edu/jmol/docs/misc/movie.spt # sample movie creation using a script # Bob Hanson [EMAIL PROTECTED] # 6:13 PM 8/16/2007 # # movie frame names are 0001, 0002, 0003, etc. # # After writing the frames, Windows movieMaker was u

Re: [Jmol-users] Thread issues in ScriptWindow

Li Yang wrote: > Hi Bob, > > > > The environment I run Jmol (V 11.2.8) on is quite sensitive and it was > able to detect a hidden thread violation from using the Run button in > the script console window. I typed a script command (for example, > spin on) in the console window, and click the

Re: [Jmol-users] ArrayIndexOutOfBoundsException and hang the viewer

I'm working on it Li Yang wrote: > Hi, > > > > I am running Jmol 11.2.8 stand alone application. Open a PDB file > (for example, 1ABT.pdb), and open the Jmol Script Console window, type > spin on, and clicked the Undo button. The viewer was *hanged* and I > could see this exception: >

Re: [Jmol-users] Animation with isosurfaces from .cube files

James, a few suggestions: First, you have to be in the frame of the model you want the isosurface for before issuing the isosurface command. And you need to give each isosurface a distinct identifier. So: frame 1 frame 1 isosurface a1 0.05 sign blue red "MO1a.cube";color isosurface translucent;

Re: [Jmol-users] dipole support for Gaussian output files

rspinney wrote: > Hi Bob, > > I want to display dipole moments and have been playing with different > file types trying to find something smaller than Spartan’s output > files. I tried a Gaussian output file and it displays bond dipole > moments ok, but it does not display the molecular dipole

Re: [Jmol-users] << Viewing Jaguar results >>

atom positions, but if you can show me that the charge data is there, we can get Jmol to read it. Or send a copy of the VIS format to [EMAIL PROTECTED], and I will see what I can do. Bob Hanson [EMAIL PROTECTED] wrote: > Hello all, > > As is descrived in the Jmol features, Jmol is c

Re: [Jmol-users] << Viewing Jaguar results >>

atom positions, but if you can show me that the charge data is there, we can get Jmol to read it. Or send a copy of the VIS format to [EMAIL PROTECTED], and I will see what I can do. Bob Hanson [EMAIL PROTECTED] wrote: > Hello all, > > As is descrived in the Jmol features, Jmol is c

[Jmol-users] list problems

testing - checking for list problems. Please do not respond. -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture

Re: [Jmol-users] dots commands

OK, thanks, Bill. That's fixed now for 11.3.10 and 11.2.9. dots 30 or dots 30% should work the same. William Reusch wrote: >Bob, > >The dotted surface around selected atoms seems to be 100% van der Waals >by default. >This may be changed by the dots (decimal) command to an equidistant >surfac

Re: [Jmol-users] more synchronization fun - 2 (mostly) different models

If possible, use commands such as: select 1.1 #select the first model translateselected rotateselected. to reorient one model to match the other. I did the following: load files "t1.pdb" "t2.pdb" frame 0 x = {71.c4*}[2].xyz - {71.c4*}[1].xyz # must use { } here, not ( ) select within(

Re: [Jmol-users] Jmol 11.3.9 -- symmetry "range" and applet synchronization

Timothy Driscoll wrote: >On Aug 7, 2007, at 11:32 PM, Bob Hanson wrote: > > > >>11.3.9 is ready for release and can be experimented with at >> >>http://chemapps.stolaf.edu/jmol/docs/examples-11 >> >>new "synchronize" command >>--

[Jmol-users] Jmol 11.3.9 -- symmetry "range" and applet synchronization

be surprised at the cross-talk between applets. So there's a new Jmol.js that goes along with this that creates a unique random sync ID for each PAGE (or FRAME) that contains applets, and delivers that to the applet as a parameter. Most people won't need jmolSetSynchId, because Jmol.j

Re: [Jmol-users] Mouse synchronization between 2 or more jmol applets

It turns out the problem is solved if you allow more than one driver. I have now implemented this, and it seems to work great. No switching necessary. Just the simple command: jmolScript("sync *") The problem I am having now is that synchronization is occuring across different web pages! But

Re: [Jmol-users] a Jaavscript question

o the page that opened it (window.opener), gets the state of that applet using opener.jmolGetPropertyAsString("stateInfo"), and clones it into its own using "script javascript:getState()". Bob Hanson Rajarshi Guha wrote: >Hi, this is not really a Jmol question, but it i

Re: [Jmol-users] css quandary with resizable applet

Frieda Reichsman wrote: >On Aug 6, 2007, at 5:58 PM, Frieda Reichsman wrote: > > > >>What I have discovered is that a height and width error are picked up >>by FF when I use the improper Jmol.js syntax for height and width of >>the applet, leaving out the brackets,that is, using (100%, 95%) >>i

Re: [Jmol-users] css quandary with resizable applet

"100%" and b = "95%" Frieda Reichsman wrote: > On Aug 6, 2007, at 6:19 PM, Bob Hanson wrote: > >> ["100%", "95%"] >> >> >> >> not >> >> >

Re: [Jmol-users] css quandary with resizable applet

["100%", "95%"] not "[100%, 95%]" Frieda Reichsman wrote: >On Aug 6, 2007, at 5:54 PM, Bob Hanson wrote: > > > >>The real problem appears to be that you are using "height=100%" for >>the >>applet but are not indi

Re: [Jmol-users] Mouse synchronization between 2 or more jmol applets

Jason Persampieri wrote: > try these: > > http://chemapps.stolaf.edu/jmol/docs/examples-11/sync.htm > http://chemapps.stolaf.edu/jmol/docs/examples-11/sync4.htm > > > Although they don't appear synchronized at all to me. > Jason, on wha

Re: [Jmol-users] Mouse synchronization between 2 or more jmol applets

I'm having a bad-url day! Yes, that's the link... [EMAIL PROTECTED] wrote: >Quoting Jason Persampieri <[EMAIL PROTECTED]>: > > > >>try these: >> >>http://chemapps.stolaf.edu/jmol/docs/examples-11/sync.htm >>http://chemapps.stolaf.edu/jmol/docs/examples-11/sync4.htm >> >>Although they don't appe

Re: [Jmol-users] css quandary with resizable applet

The real problem appears to be that you are using "height=100%" for the applet but are not indicating "height=100%" in all tables that contain it. Once that is fixed, the "noContainer" version should work. Note also that if you use overflow: auto, I think you have to specify a height. Otherwise

Re: [Jmol-users] css quandary with resizable applet

try jmolApplet(["100%", "95%"] instead of jmolApplet("100%, 95%" [EMAIL PROTECTED] wrote: >Quoting Frieda Reichsman <[EMAIL PROTECTED]>: > > > >>Anybody got a cure for these css blues? >> >>I have a Jmol layout that works solidly with the resizable applet in >>Firefox and Safari. However, i

Re: [Jmol-users] css quandary with resizable applet

those links don't work [EMAIL PROTECTED] wrote: >Quoting Frieda Reichsman <[EMAIL PROTECTED]>: > > > >>Anybody got a cure for these css blues? >> >>I have a Jmol layout that works solidly with the resizable applet in >>Firefox and Safari. However, in Internet Explorer (I know you are all >>

Re: [Jmol-users] Mouse synchronization between 2 or more jmol applets

uot;A").syncScript("off") // stop syncing I think you have to designate the slaves before you start syncing. I'm interested in whether this works better on Macs than the setTimeout polling business of compare.htm Bob Rolf Huehne wrote: >Bob Hanson wrote: > >

Re: [Jmol-users] [Jmol-developers] JMol and Firewalls

appletDocumentBase= http://jmol.sourceforge.net/demo/dots/ By the way, the "show saddles and cavities" button should be removed -- that was an early debugging capability that was removed some time ago. > Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException > at org.jmol.vi

Re: [Jmol-users] Mouse synchronization between 2 or more jmol applets

So, Egon. Can you do some investigating and see where exactly it is crashing? Bob Egon Willighagen wrote: >Bob, > >On 8/6/07, Bob Hanson <[EMAIL PROTECTED]> wrote: > > >>See http://chemapps.stolaf.edu/jmol/docs/examples-11/compare2.htm >> >>I'm

Re: [Jmol-users] Mouse synchronization between 2 or more jmol applets

it now. If someone with a Mac wants to play with compare2.htm and track down where the problem is, that would be great. Feature request. Bob Timothy Driscoll wrote: > On Aug 5, 2007, at 11:56 PM, Bob Hanson wrote: > >> Eric Martz wrote: >> >>> I surmise that it is

Re: [Jmol-users] Mouse synchronization between 2 or more jmol applets

Eric Martz wrote: >I surmise that it is still not possible to make the mouse actions >(rotate, zoom at least) in one jmol applet propagate to other >specified jmol applets on the same web page, thereby synchronizing >their mouse-controlled movements. Again, I'd like to advocate for this. > >

Re: [Jmol-users] save/write state cartoon problem

this is fixed for 11.3.8 and 11.2.8. If you need a quick fix, move the STRUCTURE commands in the state .spt information up above the MODEL STATE section. Frieda Reichsman wrote: > When I save the state or write the state to a script in Jmol 11.3.6, > areas of cartoon that are neither helix or

Re: [Jmol-users] labelling

"labels" are strictly for atoms. But "echos" can be placed anywhere. I think this is what you want. Richard Steane wrote: >Have we a facility to centre (single) labels on a number of atoms, or the >space between them? > >I am thinking of labelling R-groups on amino-acids, or labelling cavities

Re: [Jmol-users] isosurface - color command

OK, this will be fixed in 11.2.8 and 11.3.8. Thanks for pointing this out, Karl. Bob Karl Oberholser wrote: > Hi All, > > When doing solvent, sasurface or cavity with isosurface the color > command seems to have no effect. The color is a dirty yellow > regardless of what color you try to

Re: [Jmol-users] isosurface - color command

OK, I see -- there's a general bug in isosurface color I will look into it. Bob Karl Oberholser wrote: > Hi All, > > When doing solvent, sasurface or cavity with isosurface the color > command seems to have no effect. The color is a dirty yellow > regardless of what color you try t

Re: [Jmol-users] Remediated PDB format v3 vs. Jmol?

Thank you very much for doing these tests, Eric. Eric Martz wrote: >Dear Bob, > >I have now done some tests on nucleic acids for the old vs. new PDB >formats. The old format, version 2.3, has been in effect since 1998. >The new "remediated" version goes into effect August 1, 2007. >Difference

Re: [Jmol-users] save/write state cartoon problem

thanks. I'll look into that when I get back to Northfield next week. Frieda Reichsman wrote: > When I save the state or write the state to a script in Jmol 11.3.6, > areas of cartoon that are neither helix or sheet balloon up into large > tubes when the state is restored or the script is run. >

Re: [Jmol-users] information from Jmol in console

right; that's because you just set the variable "labelsgroup" to be true. That's just the way it is! Frieda Reichsman wrote: > When issuing a set command that is incorrect (and consequently has no > effect), such as > set labelsgroup > which should be > set labelgroup > > Jmol tells me > labe

[Jmol-users] nico/bob

FYI http://chemapps.stolaf.edu/jmol/docs/misc/nico_bob2.jpg -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture

Re: [Jmol-users] New menu item "Identity"?

yes, it just does set picking ident which is the default mode for picking. Eric Martz wrote: >At 7/24/07, Bob Hanson wrote: > > >>translations needed for the new "Identity" menu item. >> >> > >The only "Identity" item I find on the men

Re: [Jmol-users] using jmolSetAtomCoord

The idea is that you might want to send quite a few of these. So there is no refresh. That is, you won't see the effect until you issue a "refresh" command. The sequence I used as a test (Jmol 11.3.6) is: function test1() { jmolSetAtomCoordRelative(Math.floor(Math.random()*6),Math.random()/5-0

Re: [Jmol-users] Remediated PDB format v3 vs. Jmol?

Angel, could you please double check now and see if Jmol 11.2.5 works as you expect in this regard? translations needed for the new "Identity" menu item. Bob Angel Herraez wrote: >On 18 Jul 2007 at 15:22, Eric Martz wrote: > > >>As part of the PDB's remediation project ( >>http://remediati

Re: [Jmol-users] select/ignore with cavity in Jmol 11.2.4

load the second model, it >draws the wrong range. When I go back to the first model: wrong again. > >(I hope I am not doing something silly!) > >Christian > >P.S. Should I send you a test file? > > >On Jul 23, 2007, at 2:04 PM, Bob Hanson wrote: > > > >>

Re: [Jmol-users] select/ignore with cavity in Jmol 11.2.4

ws the wrong range. When I go back to the first model: wrong again. > >(I hope I am not doing something silly!) > >Christian > >P.S. Should I send you a test file? > > >On Jul 23, 2007, at 2:04 PM, Bob Hanson wrote: > > > >>It was a bug in the isosurfa

Re: [Jmol-users] select/ignore with cavity in Jmol 11.2.4

It was a bug in the isosurface POCKET and CAVITY subcommands. Fixed for 11.2.5 and 11.3.5 Christian Baerlocher wrote: >Hi, > >I have upgraded to Jmol 11.2.4 and now my script for the cavity >drawings in zeolites does not work properly anymore. > >I load two models from an xyz file and sele

Re: [Jmol-users] Jmol in a Spry Region

shouldn't be any issue here at all. I copied http://labs.adobe.com/technologies/spry/demos/effects/ to my hard drive, inserted an applet in the content_box, and it works OK. Putting the applet in the product_box instead produces some variation on the effects and does have an odd problem in that

Re: [Jmol-users] Adjusting Echoes for Dynamically Resizing Jmol?

Thanks for spotting that. This is fixed for Jmol 11.2.5 and 11.3.5. It was a problem with not updating the screen height and width for echo texts properly. Bob Hanson John Regner wrote: >Hey, > >I've been working on a Jmol page that employs dynamic resizing for >ever

Re: [Jmol-users] Remediated PDB format v3 vs. Jmol?

It seems to me that it is not a bug if Jmol correctly selects [DA] and [A] for group names. In addition, "select a" correctly selects for adenine, regardless of its naming. That is correct as well. That is because not all adenines are named "A" even in the standard PDB database. Angel Herr

Re: [Jmol-users] Problem with pmesh

Pmesh got broken in 11.2.0 and only just got fixed. It is fixed for 11.3.3 and 11.2.4 (to be released soon). Martin Petrek wrote: >Hello, >i was using pmesh command to visualize tunnels in proteins (in jmol >10.2.0), however it doesn't work in Jmol 11.2.3 or i'm doing something >wrong. > > >

Re: [Jmol-users] callback for draw object id?

Steven R. Spilatro wrote: >Hi all, >Is there a callback that returns the id of a draw object (line, >e.g.)? I would like to be able to click on a line and retrieve its >id number. If not, might this function be developed? > > You can "fake" this with a callback for an invisible (transluce

Re: [Jmol-users] sample page for surfaces

've forgotten how to do it) Bob > >On Jul 1, 2007, at 1:54 AM, Bob Hanson wrote: > > > >>Here is a sample page for surfaces. Not comprehensive; just gives a >>bunch of examples. >> >>http://chemapps.stolaf.edu/jmol/docs/examples-11/surfacedemos.

Re: [Jmol-users] sample page for surfaces

I think you could create such a thing, but it's not something that we provide automatically. Sounds like something that could be done with the menu, perhaps. Feature request Mark Williamson wrote: >Bob Hanson wrote: > > >>Here is a sample page for surfaces. Not compr

[Jmol-users] sample page for surfaces

Here is a sample page for surfaces. Not comprehensive; just gives a bunch of examples. http://chemapps.stolaf.edu/jmol/docs/examples-11/surfacedemos.htm Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answ

[Jmol-users] major goof

Jmol Users. 11.2.1 is majorly flawed. I have removed it from the release list. Same for 11.3.2. We'll get a new set up as soon as we can. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what w

Re: [Jmol-users] lcaocartoons for sp3d2 hybrid orbitals (octahedral coordination)?

;;-) > >- Original Message - >From: Bob Hanson <[EMAIL PROTECTED]> >Date: Wednesday, June 27, 2007 1:56 pm > > > >>no plans for that. I figured one could set that up with lobes. The >>problem is defining the different directions. sp, sp2, sp3 are har

Re: [Jmol-users] Access problems with Jmol content

Nick, have you put XML headers at the top of your page, or are you doing something like ? That would be my guess, as there is no document object and no applet object, either, based on this message: jsoDocument returned null ... no DOM manipulations :-( That's a message from Jmol indicating

Re: [Jmol-users] Problem about JMOL

Liu hai, I've forwarded this reply to Jmol-users, because I think others would be interested in it. All: Liu hai has a mol2 file with comments at the beginning. This tricked Jmol into thinking it was a MOL file rather than a MOL2 file. If you are ever in this situation where you know a file h

Re: [Jmol-users] Bonds as first class jmol citizens

Aidan, You CAN select bonds, but it's not advertised. To see how it's done, do something with a few selected bonds (color them, for instance) and then do show state you will see how Jmol 11 allows selecting bonds and manipulating them as entities. No labels, no pick. If you want to label and

Re: [Jmol-users] java.lang.OutOfMemoryError: Java heap space in APPLET

on't use a second buffer. Bob Raphael A. Bauer wrote: >Bob Hanson wrote: > > >>2:1 you have a Mac. In any case, you need to find the control panel for >>Java and increase the allowed memory. Others on the list can help you >> >> >... >unix lik

Re: [Jmol-users] write coords XYZ

just select the models you want to write. select 1.1 write coord XYZ "model1.xyz" select 1.2 write coord XYZ "model2.xyz" etc. Sebastian Schwieger wrote: >Dear jmol team, > >I was trying to write xyz coordinates of a specific frame from an >optimization done with gaussian. >Using "write coords

Re: [Jmol-users] java.lang.OutOfMemoryError: Java heap space in APPLET

2:1 you have a Mac. In any case, you need to find the control panel for Java and increase the allowed memory. Others on the list can help you figure out how to do that if you don't know how. Raphael A. Bauer wrote: >Raphael A. Bauer wrote: > > >>hi jmol list, >> >>i am constantly getting out

Re: [Jmol-users] Bugs in 11.2.0-11.3.0: hover, zoomto (center)

part II hover. fixed for 11.2.2, 11.3.1 We saw problems with hover being interrupted in earlier prereleases of Jmol. I thought I had fixed it at that time, but I guess not. I've now set it to restart the thread if it gets interrupted whenever the mouse is moved. Eric, when this is released, ple

Re: [Jmol-users] Bugs in 11.2.0-11.3.0: hover, zoomto (center)

Two replies -- one for hover, one for zoomto. This one is zoomto: Eric Martz wrote: >Dear Bob, > >2. "zoomto" with no parameters fails to zoom 2X as it did in earlier >versions. Similarly, "zoomto out" does not change the zoom in 11.3.0. > >3. zoomto (center) results in an incorrect center when

Re: [Jmol-users] lcaocartoons for sp3d2 hybrid orbitals (octahedral coordination)?

no plans for that. I figured one could set that up with lobes. The problem is defining the different directions. sp, sp2, sp3 are hard enough to specify. sp3d2 I gave up. These should be able to be set up with combinations of isosurface LOBE commands. Give that a try at least. Phillip Barak

Re: [Jmol-users] how to accelerate command script?

ay, on a 0-100 scale -- and then use that number. Might work. Bob Hanson Garnier Nicolas wrote: > hi, > I'm using Jmol with proteins that can be more than 800 residues. I > have some specific colorations where each residues can take a color. > So it's very long to color each

Re: [Jmol-users] centering echo

It's just the way it is designed. The attachment point is the bottom of the text in all cases. The top echo is working because Jmol makes sure the text is not off-screen and so adjusts it downward. You can get it more centered using something like: set echo myecho 50% 45% set echo myecho center

Re: [Jmol-users] applet params

If you don't mind digging through a bit of code, all applet tags are handled by a single function: There is a comment at the top that purports to list them all; this may or may not be fully inclusive.

Re: [Jmol-users] translucent lcaoCartoons? sure!

not a bug, but also not intuitive and probably not well described in the documentation. LcaoCartoons are different from other isosurfaces in that they have multiple component parts at a given atom and generally one wants to set the color and translucency up front, before any are drawn, and then

[Jmol-users] new draw capability

Jmol 11.3.0 will have the capability to select specific vertexes from a drawn object: draw p plane perp (atomno=1) (atomno=2) pointCenter = $p #average point1 = $p[1] point2 = $p[2] point3 = $p[3] point4 = $p[4] Then you can do things like: draw p1 @point1 rotate 10 $p[2] $p[4] etc. --

Re: [Jmol-users] User-positioned echo trapped in window

n the user hovers over one of the points associated with the draw object. If more complex, colored, or translucent text is desired, use ECHO instead: set echo myecho {3 4 5} echo "some | more complex | text" color echo translucent white Bob Rolf Huehne wrote: >Rolf Huehne wrote: >

Re: [Jmol-users] User-positioned echo trapped in window

off using draw text1 on draw text1 off Bob Hanson Rolf Huehne wrote: > Dear all, > >I try to label draw objects like planes. Currently the only way to do >this seems to be with a user-defined echo positioned at a >three-dimensionsonal coordinate. > >First of all I n

[Jmol-users] [Fwd: Jmol -Regarding Jmol.js file]

Please refer your question to the jmol-user list. Thank you. Original Message Subject:Jmol -Regarding Jmol.js file Date: Mon, 18 Jun 2007 14:22:56 +0530 From: TK.Jiji <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Dear Sir, When i was running JmolApplet.java file

[Jmol-users] Jmol 11.2 released

Jmol users: Jmol 11.2 has been released. The following list summarizes the changes since the most recent release, Jmol 11.0. Please note that the default perspective model has been set to 11 instead of 10. This means that users who are installing this release in web sites now using earlier ver

Re: [Jmol-users] wireframeRotation

Wow, no kidding? Jmol 7! That option is long gone -- considered unnecessary. Frieda Reichsman wrote: > Hi, > > I can across a web page, > http://www.chm.bris.ac.uk/motm/acetylcoa/acoajm.htm > > and noticed a Jmol effect I had not seen before, wireframeRotation. > (Just rotate any structure on th

Re: [Jmol-users] Orient molecule along bond or arbitrary axis

e line instead of either end. I guess I can always pass the >information to Jmol using Javascript, since that's how I created the line in >the first place. > > > >Dean > > >On 6/15/07 12:58 AM, "Bob Hanson" <[EMAIL PROTECTED]> wrote: > >

Re: [Jmol-users] Orient molecule along bond or arbitrary axis

This is better -- it uses improper angles to set the sign of the angle correctly. Bob Hanson wrote: >no simple way. HOWEVER, you could do the calculation I think. Let's see >if it can be done with a Jmol script... > >Let's say we want to align the axis between atom 1 an

Re: [Jmol-users] Orient molecule along bond or arbitrary axis

want to be able to "look down" a particular molecular axis - so >I guess that might be "orient this bond along the Z axis". > >Dean > > >On 6/14/07 10:45 PM, "Bob Hanson" <[EMAIL PROTECTED]> wrote: > > > >>Dean, >> >&

Re: [Jmol-users] Orient molecule along bond or arbitrary axis

the X (horizontal) axis"? Bob Hanson Dean Johnston wrote: >Jmol users, > > Does anybody know a simple way to align a molecule in the Jmol viewer >along a bond or (arbitrary) axis? This axis may not correspond to one of >the original x, y, or z axes. (or front, back, to

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

It's also, I think, only with the Jmol application, not the applet. OK, let's let it go. Bob Sérgio Ceroni da Silva wrote: > >>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 de

Re: [Jmol-users] Polyhedra with 12 or 20 vertices

l and triangles/quadrilaterals, and you will get there faster. You can load a file of coordinates and work with it to draw just about anything you want, provided the objects are triangles or quadrilaterals. Pmesh is another command that comes to mind. Bob >Dean > > >On 6/9/

Re: [Jmol-users] jmol and overlay data

; and fit into a select command then as: otherFile = 3 - thisFile select atomno=mappedAtom and file=otherFile Something like that If you want to display both models side-by-side instead of on top of each other, you might consider doing something like: load files "model1.sdf" &q

Re: [Jmol-users] RotateSelected

Michael, We are within days of releasing 11.2, and that is why the documentation got a bit ahead of us. Just go to the download page and select 11.1.48 Bob Hanson [EMAIL PROTECTED] wrote: >Hello, > >I tried to use the RotateSelected function, but it doesn't work. In the >docu

Re: [Jmol-users] problem with spin after loop and quit

good catch -- simple fix. 11.1.49 Frieda Reichsman wrote: > It seems that after issuing a script with a loop command: > move 0 -30 0 0 0 0 0 0 2.0 > move 0 30 0 0 0 0 0 0 2.0 > loop on > > I cannot get the structure to spin using > quit; spin on > > until I either > - click in the applet, or >

Re: [Jmol-users] Animation: pause/resume, and unwanted frame skipping

Eric Martz wrote: >In >contrast, "anim on" restarts from the first frame. > > > and resets the frame range to "all models" - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 e

Re: [Jmol-users] 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 changed >javaw uses more 6 to 15 MB. This happen with every langu

Re: [Jmol-users] 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 changed >javaw uses more 6 to 15 MB. This happen with every langu

Re: [Jmol-users] Polyhedra with 12 or 20 vertices

Dean, sounds like you might appreciate: http://www.scienceu.com/geometry/facts/solids/coords/ Well, ah, let's just say it doesn't work the way you probably think it does. The polyhedra code is a very complex algorithm that looks at possible faces (combinations of three atoms around a central at

Re: [Jmol-users] Jmol applet - crash with inline model (OS X)

up an example page (it's currently just running >locally). > >Dean > > >On 6/8/07 10:39 PM, "Bob Hanson" <[EMAIL PROTECTED]> wrote: > > > >>Dean, please send me the script. I'd like to fix this. >> >>Dean Johnston wrote: &g

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

I wholeheartedly support this discussion. Jmol 10 WAS strictly a "molecular viewer" -- there is no question about that. It's intriguing to think that Jmol 11 is "more than a molecular viewer" because of the additional capabilities in the area of crystallography. Personally I don't see the dist

Re: [Jmol-users] Jmol applet - crash with inline model (OS X)

Dean, please send me the script. I'd like to fix this. Dean Johnston wrote: > I’m getting an odd (and hard to reproduce) crash with the Jmol applet > (Firefox or Safari on OS X, version 11.1.48_dev). I try and load an > inline model and sporadically get the error listed below. It seems to > al

Re: [Jmol-users] Animation: pause/resume, and unwanted frame skipping

Eric Martz wrote: >QUESTION 2: SKIPPING FRAMES. > >When I run the Chime animation concurrently with the Jmol animation >(in the same or different browsers), Jmol's animation skips frames. I >interpret this to mean that when the CPU is heavily loaded, Jmol >skips frames. Perhaps frames would als

Re: [Jmol-users] questions

rspinney wrote: > >I'm not sure we are on the same wavelength. As an example, frame 20 is a >"key" frame where echo and message are changed. If the animation is >"playing" (i.e. using "animation direction +1; model resume;") the changes >(based on the frame number) are caught by animFrameCallback

Re: [Jmol-users] Help with Jmol

David, you might also be interested in a site we developed here at St. Olaf, as it has about 1000 small molecules; http://www.stolaf.edu/depts/chemistry/mo/struc/ with associated model files in http://www.stolaf.edu/depts/chemistry/mo/struc/data/ Bob Hanson David Kim wrote: > Hello, >

[Jmol-users] perspective model default

perspective.htm Consider your own pages, and how much trouble it would be to add "set perspectiveModel 10" to them if you feel that would be necessary. Then get back to us. Thank you, Bob Hanson -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.st

Re: [Jmol-users] Keeping track of all jmol features?

I have added inline help capability to the Jmol application for 11.1.46. help or help #targets that particular command or just help#does a search Bob Thank you, Nico! Nicolas Vervelle wrote: > Bob Hanson a écrit : > >> This is about as close as we are going to come

Re: [Jmol-users] questions

rspinney wrote: >I have a couple of questions for Bob. (I am using 11.1.44.) > >1) I am not clear if frame (or model) next or previous make a call to >animFrameCallback. I have a jmolSetCallback linked to animFrameCallback, and >it works fine for model play, pause and resume (which will execute a

Re: [Jmol-users] problem exporting to script file

tegration >of Jmol in other applications. > >Cheers, > > .../Ola > >On May 31, 2007, at 19:35 , Bob Hanson wrote: > > > >>Thanks, Angel. This is fixed for 11.1.45. >> >>Nico, can you see if there is a simple way of having the export file >&g

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