Re: [Jmol-users] help displaying jvxl MO

2010-01-24 Thread Robert Hanson
Bob, I'll be very interested in seeing what you end up with. A couple more thoughts on this I did some tests, and there are two problems. First, the data are definitely mangled. I see escape sequences that should not be there -- \/ -- (escape FORWARD slash) for example, and there must be somet

Re: [Jmol-users] help displaying jvxl MO

2010-01-23 Thread Grossman, Robert B
Ah, I see. And the .jvxl file that my friend sent me must have been created by Jmol from a QM calculation that my friend had generated with WebMO and loaded into Jmol. So when he was trying to make my life easier by sending me the .jvxl file instead of the WebMO results file, he was really mak

Re: [Jmol-users] help displaying jvxl MO

2010-01-23 Thread Robert Hanson
On Sat, Jan 23, 2010 at 9:33 PM, Grossman, Robert B wrote: > We can let Jmol create the MO from the QM data in the browser - I think > that is what we are doing now with the .mo file - but we greatly prefer to > read the QM data from the database, not from a file. > > I'm still trying to understa

Re: [Jmol-users] help displaying jvxl MO

2010-01-23 Thread Grossman, Robert B
We can let Jmol create the MO from the QM data in the browser - I think that is what we are doing now with the .mo file - but we greatly prefer to read the QM data from the database, not from a file. I'm still trying to understand the mutual dependencies among load, isosurface, and mo. When I

Re: [Jmol-users] help displaying jvxl MO

2010-01-23 Thread Robert Hanson
I think it just got mangled as being part of the email. isosurface is used to create MOs from files that are not QM files. -- surfaces. mo is used to generate the MO data directly from the basis functions. Most people these days, I think, just let Jmol read the QM file and create the MO in the bro

Re: [Jmol-users] help displaying jvxl MO

2010-01-23 Thread Grossman, Robert B
Hi Bob, The information is read from an Oracle database and written into a JSP page. We have the ability to write information to files, but we want very much to avoid having to do it. We also want to avoid having to deal with multiple files to display a single molecule and its associated MOs

Re: [Jmol-users] help displaying jvxl MO

2010-01-23 Thread Robert Hanson
Well, two things. First, you must have mangled the data some way - or at least clipping from this page doesn't work. Because the attached file did run. Second, you can only load an isosurface "inline" like that in the very latest version of Jmol. (I'm not sure it's even in the one I have up at http

[Jmol-users] help displaying jvxl MO

2010-01-20 Thread Grossman, Robert B
Hi, I have a JVXL file containing MO data that I am trying to display. I can see the molecule, but I can't see the MO. I have tried various scripts to turn on the MO, to no avail. Below I have copied the relevant part of my Web page. I am using 'mo HOMO;' as the script, but I have tried sev

Re: [Jmol-users] help needed -- crystallography

2009-08-24 Thread Robert Hanson
first select a model, then do the other things. Bob On Mon, Aug 24, 2009 at 9:06 AM, Alexander Klenner < klen...@bioinformatik.uni-frankfurt.de> wrote: > I am not sure if it's me but the applet won't work at my computer. > > java.io.FileNotFoundException: > http://chemmaps.stolaf.edu/jmol/docs/

Re: [Jmol-users] help needed -- crystallography

2009-08-24 Thread Alexander Klenner
I am not sure if it's me but the applet won't work at my computer. java.io.FileNotFoundException: http://chemmaps.stolaf.edu/jmol/docs/examples-11/jcse/zapped Alex Robert Hanson schrieb: > I would appreciate crystallography-minded users checking out > > http://chemapps.stolaf.edu/jmol/docs/exam

[Jmol-users] help needed -- crystallography

2009-08-22 Thread Robert Hanson
I would appreciate crystallography-minded users checking out http://chemapps.stolaf.edu/jmol/docs/examples-11/showsym.htm this page allows visualization of all symmetry operations. I think it is working properly; would like confirmation of that. Bob -- Robert M. Hanson Professor of Chemistry

Re: [Jmol-users] Help with Jmol and jQuery?

2009-05-28 Thread Jeff Hansen
Thanks to everyone for helping with this. I understand where I was going wrong and I've got things in much better shape now. I have another question. I've pulled data out of the file loaded into Jmol and used it to plot points in an svg element. I would like to use jQuery to access thos

Re: [Jmol-users] Help with Jmol and jQuery?

2009-05-27 Thread Robert Hanson
Interesting idea. Probably without the points would be nicer. On Wed, May 27, 2009 at 4:43 PM, Xavier Prat-Resina wrote: > Not sure if it's useful, I'm using jQuery/flot here > http://www.chemeddl.org/collections/molecules/index.php > click the IR spectrum button and a flot chart pops up > > Xavi

Re: [Jmol-users] Help with Jmol and jQuery?

2009-05-27 Thread Xavier Prat-Resina
Not sure if it's useful, I'm using jQuery/flot here http://www.chemeddl.org/collections/molecules/index.php click the IR spectrum button and a flot chart pops up Xavier On Wed, May 27, 2009 at 3:37 PM, Robert Hanson wrote: > Jeff, I'm using jQuery at > > http://chemapps.stolaf.edu/jmol/docs/exa

Re: [Jmol-users] Help with Jmol and jQuery?

2009-05-27 Thread Robert Hanson
Jeff, I'm using jQuery at http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot.htm and http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm I'm sure your problems do not arise from Jmol.js. The jQuery business is quite well modularized. Bob On Wed, May 27, 2009 at 11:

Re: [Jmol-users] Help with Jmol and jQuery?

2009-05-27 Thread Jeff Hansen
Andreas, It looks to me like some kind of timing issue. I've made a page with some jQuery stuff on it. It works. I add a Jmol applet. Everything still works. I then put a function that grabs data from the Jmol applet inside the (document).ready wrapper and put a call to that function

Re: [Jmol-users] Help with Jmol and jQuery?

2009-05-27 Thread Andreas Prlic
Hi Jeff, Now sure what's exactly the problem from your description, perhaps you can send some example code? We are using a mix between JQuery and self written javacript on the new RCSB-PDB web site: e.g. this page tracks the Jmol console output to a div and shows the command history: http://www.

[Jmol-users] Help with Jmol and jQuery?

2009-05-27 Thread Jeff Hansen
Does anyone have any experience using jQuery on a page with Jmol? I wanted to do this as it would greatly simplify some things I wanted to do. Unfortunately, none of the jQuery seems to be working. Let me explain. I can load a Jmol applet and structure and write javascript to manipulate

Re: [Jmol-users] Help

2009-01-09 Thread Angel Herraez
Hi Phan I agree with Duan. It may be a problem with the file path. Open the Java console and copy the exact error, and post it here. For a safest test, put the pdb file and the Jmol.jar file in the same folder, then open the script console and type load yourfile.pdb (do not use the top menu,

Re: [Jmol-users] Help

2009-01-08 Thread Duan Lian
Hi, Phan Does the path of the PDB file contains any Chinese/Japanese/Korean characteristics? I have seen this kind of problem before. Best Regards, Duan Lian Laboratory of Molecular Modeling and Design School of Pharmacy East China University of Science and Technology Shanghai, 200237, China O

[Jmol-users] Help

2009-01-08 Thread phuong h. phan
Hi, I am new user of Jmol. I downloaded Jmol today, installed and started to use it. I want to see the protein 3D structure so I download one .pdb file from Protein Data Bank website. But Jmol could not show its 3D figure while RasMol can do it. On the screen of Jmol, It said that: java.io. File N

Re: [Jmol-users] Help with xyz-file

2008-12-23 Thread Robert Hanson
You are just missing an information line -- the second line. On Tue, Dec 23, 2008 at 5:53 AM, A. Dijkman wrote: > Hi there, > > I'm new to scripting and I want to make a movie of a esterification. I made > the first scene with an xyz-file (see below). For some reason Jmol doesn't > show the first

[Jmol-users] Help with xyz-file

2008-12-23 Thread A. Dijkman
Hi there, I'm new to scripting and I want to make a movie of a esterification. I made the first scene with an xyz-file (see below). For some reason Jmol doesn't show the first carbon atom in this list. Can somebody help me? 14 C 25.6657 -8.8104 0. O 24.2556 -8.7796 -0.1649 H 26.1547 -8.8211

Re: [Jmol-users] help needed -- bonding radii of anions

2008-09-17 Thread Robert Hanson
I have added most of those values. I have to make O- smaller, though, or it doesn't work correctly in organic compounds. Perhaps some testing this M(OH)x would be in order. Bob On Wed, Sep 17, 2008 at 12:55 PM, Phillip Barak <[EMAIL PROTECTED]> wrote: > Since Angel has added in coordination num

Re: [Jmol-users] help needed -- bonding radii of anions

2008-09-17 Thread Phillip Barak
Since Angel has added in coordination numbers, I'll add in Shannon's values (1976) for comparison, which seem to be the source for some of the 77th edn values: - Original Message - From: Angel Herraez <[EMAIL PROTECTED]> > In case it is of help, I found in our library a 56th edition (19

Re: [Jmol-users] help needed -- bonding radii of anions

2008-09-17 Thread Angel Herraez
In case it is of help, I found in our library a 56th edition (1975- 76) and a 77th edition (1996-97) of the CRC Handbook of Chemistry and Physics. Both have tables entitled "CRYSTAL IONIC RADII OF THE ELEMENTS" (pages F209 to F210 and 12-14 to 12-15 respectively) with these values: > > (8

Re: [Jmol-users] help needed -- bonding radii of anions

2008-09-17 Thread Phillip Barak
vol:32 iss:SEP1 pg:751 -767 Hope this helps, --Phil Barak - Original Message - From: Robert Hanson <[EMAIL PROTECTED]> Date: Tuesday, September 16, 2008 10:58 pm Subject: [Jmol-users] help needed -- bonding radii of anions To: jmol-users@lists.sourceforge.net > Jmol has some very

[Jmol-users] help needed -- bonding radii of anions

2008-09-16 Thread Robert Hanson
Jmol has some very odd bonding radii for unusual anions. Note the numbers: (8 << 4) + (-2 + 4), 1320, // "O-2" (8 << 4) + (-1 + 4), 1760, // "O-1" // WAY too large? (14 << 4) + (-4 + 4), 2710, // "Si-4" (14 << 4) + (-1 + 4), 3840, // "Si-1" // same problem here? (34 << 4) +

Re: [Jmol-users] Help with Jmol

2007-06-05 Thread Paul Pillot
For small molecules, you can use this website : http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ It allows to design small molecules through the JRE applet and calculates a minimized energy model. Other websites such as Klotho or Drugbank are great for organic molecules. Paul David Kim a écrit

Re: [Jmol-users] Help with Jmol

2007-06-05 Thread Bob Hanson
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, > > My

Re: [Jmol-users] Help with Jmol

2007-06-05 Thread Angel Herraez
(I have answered to David through the developers list) - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get

[Jmol-users] Help with Jmol

2007-06-05 Thread David Kim
Hello, My name is David Kim and I am currently an employee of the National Center for Supercomputing Applications. I am currently working in the Education department and we are trying to incorporate Jmol into one of our workshops. The program is called ICLCS and we are trying to assist teachers i

Re: [Jmol-users] help requested - summary of additions in Jmol 11

2007-05-14 Thread Rolf Huehne
Angel Herraez wrote: > Dear Jmol users, > I want to update the History page on Jmol's web, to include the improvements > made in > Jmol since 10.2. I'm entitling that "Jmol outgrows Chime". > Bob recently posted a message summarizing some of the new features, and there > is an > extensive detai

[Jmol-users] help requested - summary of additions in Jmol 11

2007-05-13 Thread Angel Herraez
Dear Jmol users, I want to update the History page on Jmol's web, to include the improvements made in Jmol since 10.2. I'm entitling that "Jmol outgrows Chime". Bob recently posted a message summarizing some of the new features, and there is an extensive detailed list of changes in his website,

Re: [Jmol-users] Help for a Complete Beginner

2007-05-06 Thread Patrick J. Carroll
Steve, I have been using Jmol and javascript to design web pages that will enable users to build crystal packing diagrams. See, for example: http://macxray.chem.upenn.edu/cells/7014SG.html Pat Carroll U Penn X-ray Facility --

Re: [Jmol-users] Help for a complete beginner -- ?NOAPPLET and XTAL

2007-05-06 Thread Paul Pillot
Once you've loaded your structure, you must open the Jmol command line (using the right mouse button for example) and type : load "" {3 2 2} if you want 3 x 2 x 2 unitcells. Hope this help, Paul - This SF.net email is sponso

Re: [Jmol-users] Help for a complete beginner -- ?NOAPPLET and XTAL

2007-05-06 Thread Bob Hanson
ahem, and clicking those links I see 11.1.32 has a bug in the draw business that is displaying its command as text!!! Look for 11.1.33 soon :) Bob Hanson wrote: >oops, make that: > >http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/xtal.htm > >Bob > > >Bob Hanson wrote: > > >

Re: [Jmol-users] Help for a complete beginner -- ?NOAPPLET and XTAL

2007-05-06 Thread Bob Hanson
oops, make that: http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/xtal.htm Bob Bob Hanson wrote: >Welcome, Stephen, > >First thing to know is that if you don't know how to do anything at all > >1) search for it in http://www.stolaf.edu/academics/chemapps/jmol/docs > >2) ask this

Re: [Jmol-users] Help for a complete beginner -- ?NOAPPLET and XTAL

2007-05-06 Thread Bob Hanson
Welcome, Stephen, First thing to know is that if you don't know how to do anything at all 1) search for it in http://www.stolaf.edu/academics/chemapps/jmol/docs 2) ask this list NOT necessarily in that order! (It's a very friendly list, and the documentation can be overwhelming.) In this cas

Re: [Jmol-users] Help for a complete beginner

2007-05-06 Thread Angel Herraez
Welcome, Stephen I'm a biochemist, so no expert at crystallographic matters, but I think this is what you need: http://www.stolaf.edu/academics/chemapps/jmol/docs/examples- 11/sym.htm It's linked on the right side from Bob's Jmol page, http://www.stolaf.edu/academics/chemapps/jmol/ If you wish,

[Jmol-users] Help for a complete beginner

2007-05-06 Thread Stephen Hillier
Hi, I am trying to learn how to use the Jmol standalone application to display mineral structures. I have downloaded several structures form online mineral structure databases and can load them into Jmol succesfully, but what I don't understand is how to start adding/replicating atoms to start fi

Re: [Jmol-users] help

2007-03-23 Thread Angel Herraez
Hi Vivi In principle, you include the path together with the filename:    jmolApplet(350,"load /whatever/path/is_your_file/S_0003_8934_0001.pdb"); However, using absolute paths is delicate, due to Java security restrictions. That will only work from web server, n

[Jmol-users] help

2007-03-23 Thread 张倩
Hi, Now I have a question about how to use the "load" method to load a file. I use this method like tihs in HTML: . jmolApplet(350,"load S_0003_8934_0001.pdb"); but if the S_0003_8934_0001.pdb and the HTML file are not in the same path, How can I use this command? I want to us

Re: [Jmol-users] help

2007-03-19 Thread Angel Herraez
Hi Vivi I don't know if it can be done as you are trying, but I suggest two solutions: 1) Why aren't you using Jmol.js? Things are much easier with it. a) You load Jmol.js library: b) You insert the applet: jmolInitialize("./")

[Jmol-users] help

2007-03-19 Thread 张倩
Hi, I have a question of using Jmol to reload a pdb file. My idea is: if I have another pdb file, for example: 1.pdb, and I want the HTML to reload the new pdb file automatically. I use the code below to actualize my idea, but it can't work. The code is : Image

Re: [Jmol-users] Help using Jmol Applet?

2006-04-22 Thread Rick Muller
Thanks, Angel. Rick On Apr 22, 2006, at 8:21 AM, Angel Herraez wrote: Rick, I copied the code from your previous message and it works with both jmolInitialize(".") or jmolInitialize("./") I think you have a problem with the folders. This is my setup: A folder where the page is and where th

Re: [Jmol-users] Help using Jmol Applet?

2006-04-22 Thread Angel Herraez
Rick, I copied the code from your previous message and it works with both jmolInitialize(".") or jmolInitialize("./") I think you have a problem with the folders. This is my setup: A folder where the page is and where the applet files are (JmolApplet0.jar to 6.jar, plus Jmol.js). Below it, a fo

It works now... (was: Re: [Jmol-users] Help using Jmol Applet?)

2006-04-22 Thread Rick Muller
I put up the pages at http://wag.caltech.edu/home/rpm/JmolGalleryeverything seems to work now, for some reason. Can't really figure what I've changed.But thanks for everyone's help.RickOn Apr 22, 2006, at 8:06 AM, Angel Herraez wrote: On 22 Apr 2006 at 7:10, Rick Muller wrote: > I tried to initial

Re: [Jmol-users] Help using Jmol Applet?

2006-04-22 Thread Angel Herraez
On 22 Apr 2006 at 7:10, Rick Muller wrote: > I tried to initialize with > jmolInitialize("."), but that didn't work, so I just called the local directory (Gallery) using "../Gallery". > What's the right way to do this? try jmolInitialize("./") -

Re: [Jmol-users] Help using Jmol Applet?

2006-04-22 Thread Rick Muller
Right, it uses a different application called MolApp.jar. I'm just trying to get the current version working on my local drive before I put it up on the web page. R. On Apr 22, 2006, at 7:24 AM, Bob Hanson wrote: Not Found The requested URL /home/rpm/gallery/JmolApplet0.jar was not foun

Re: [Jmol-users] Help using Jmol Applet?

2006-04-22 Thread Bob Hanson
Not Found The requested URL /home/rpm/gallery/JmolApplet0.jar was not found on this server. Rick Muller wrote: Bob, Thanks for your quick reply. On Apr 21, 2006, at 3:24 PM, Bob Hanson wrote: 1) I don't see the necessary there. It's there, and sorry for the confusion. I just didn

Re: [Jmol-users] Help using Jmol Applet?

2006-04-22 Thread Rick Muller
Bob, Thanks for your quick reply. On Apr 21, 2006, at 3:24 PM, Bob Hanson wrote: 1) I don't see the necessary there. It's there, and sorry for the confusion. I just didn't include it because I wanted to be terse, which was a mistake. Here's the whole page: Molecular Gallery

Re: [Jmol-users] Help using Jmol Applet?

2006-04-22 Thread Rick Muller
Angel,Thanks for your quick response. Actually, the files *are* in the same branch. I tried to initialize with jmolInitialize("."), but that didn't work, so I just called the local directory (Gallery) using "../Gallery". What's the right way to do this?R.On Apr 21, 2006, at 5:58 PM, Angel Herraez w

Re: [Jmol-users] Help using Jmol Applet?

2006-04-21 Thread Timothy Driscoll
On Apr 21, 2006, at 7:58 p, Angel Herraez wrote: It looks to me that you have the applet files on a different branch folder ../Gallery/JmolApplet0.jar than the molecule files gallery/c2h4.xyz how about case, too? sometimes Gallery = gallery, and sometimes not. tim -- Timothy Driscoll

Re: [Jmol-users] Help using Jmol Applet?

2006-04-21 Thread Angel Herraez
Hello Rick Are you testing from a web server, or from your hard disk? Java imposes security constraints for local files (explained at http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local It looks to me that you have the applet files on a different branch folder ../Gallery/JmolApplet0

Re: [Jmol-users] Help using Jmol Applet?

2006-04-21 Thread Bob Hanson
1) I don't see the necessary there. 2) Are JmolApplet0.jar - JmolApplet6.jar in http://www.wag.caltech.edu/home/rpm/Gallery ? Rick Muller wrote: A long time ago I put together a molecular gallery web page at: http://www.wag.caltech.edu/home/rpm/gallery This used a little Java applet

[Jmol-users] Help using Jmol Applet?

2006-04-21 Thread Rick Muller
A long time ago I put together a molecular gallery web page at: http://www.wag.caltech.edu/home/rpm/gallery This used a little Java applet that I wrote myself, and used JavaScript calls to update the molecule when the drop-down menu changed I'd like to update this to use JmolApplet. I've trie

Re: [Jmol-users] Help with creating a file

2006-02-20 Thread Timothy Driscoll
On Feb 19, 2006, at 7:46 p, Jeff Hansen wrote: We are working on a project in which we would like to use Jmol to visualize hemoglobin and animate how the structure changes when oxygen binds. Does anyone have any suggestions of how we could generate the necessary pdb or xyz file? I'm guess

Re: [Jmol-users] Help with creating a file

2006-02-20 Thread Bob Hanson
Jeff, is your intent to produce a cartoon that (a) pretends to describe the actual change or (b) something that is based on some actual intermediary data of some sort in addition to the known two structures? I can see how the boundaries might get blurred here in the presentation. I'll be inte

[Jmol-users] Help with creating a file

2006-02-20 Thread Jeff Hansen
We are working on a project in which we would like to use Jmol to visualize hemoglobin and animate how the structure changes when oxygen binds. Does anyone have any suggestions of how we could generate the necessary pdb or xyz file? I'm guessing it would require some kind of molecular dyn

[Jmol-users] Help

2005-08-09 Thread Freddy A. Rojas P.
Hi, I want to know if I can view NWChem's input or output files with Jmol? If it possible to view these files, anybody could send me some samples files? Thanks Freddy A. Rojas P. smime.p7s Description: S/MIME cryptographic signature

[Jmol-users] Help

2005-08-09 Thread Freddy A. Rojas P.
Hi, I want to know if I can view NWChem's input or output files with Jmol? If it possible to view these files, anybody could send me some samples files? Thanks Freddy A. Rojas P. smime.p7s Description: S/MIME cryptographic signature

RE: [Jmol-users] Help

2005-07-12 Thread Miguel
> Clearly that is your choice, since you want to access pdb files from > elsewhere. On the other hand, I understand that all this trouble only > applies to local files, so if you serve the files form the web server > any method should work (as long as you have the relative paths > correct). You sh

RE: [Jmol-users] Help

2005-07-12 Thread Miguel
> Hi everyone!, first at all thanks for your support. > > I tried Angel's first option and it didn't work out, the second one did > it. > But I'm inserting the html code into a jsp which belong to a portlet which > will be run on a tomcat's portal. The main idea is to put Jmol as an > external dir

RE: [Jmol-users] Help

2005-07-12 Thread Angel Herraez
Freddy, as far as I know, the signed applet is loaded in the same way as the non-signed one, just call JmolAppletSigned.jar instead of JmolApplet.jar I've never used it, though. Clearly that is your choice, since you want to access pdb files from elsewhere. On the other hand, I understand that all

RE: [Jmol-users] Help

2005-07-12 Thread Freddy A. Rojas P.
Hi everyone!, first at all thanks for your support. I tried Angel's first option and it didn't work out, the second one did it. But I'm inserting the html code into a jsp which belong to a portlet which will be run on a tomcat's portal. The main idea is to put Jmol as an external directory of thi

Re: [Jmol-users] Help for a beginner, please

2005-07-12 Thread Angel Herraez
Hello, Russ Sorry for the empty message, I didn't realize. It's happened a couple times now. I am recalling some trouble with my smtp server being banned from SF, may be that. I am copying the message: Hi, Russ. Welcome tom the exciting world of molecular visualization > I've figured out how to d

Re: [Jmol-users] Help

2005-07-11 Thread timothy driscoll
On 2005-07-11 (21:57) Angel Herraez wrote: >On 11 Jul 2005 at 15:34, Freddy A. Rojas P. wrote: > >>Windows and Unix but, in both cases I could load the applet but not >>the molecule. I tried to load the molecule from applet's console but >>I got an I/O Exception. Can you tell me what I'm doing wro

Re: [Jmol-users] Help

2005-07-11 Thread Angel Herraez
Hi, Freddy Sounds like the eternal problem of accessing local files from Java; the files must be in a folder equal or below the applet. Try to move the xyz file:    Simple example