From: Nkemdilim U. <Nke...@gm...> - 2005-01-26 10:42:52
|
Hi, My name is Nkemdilim Uwaje and I am a bioinformatics student at the LMU in Munich and I am trying to develop a graphic user interface (using Java) for a chemical library that I am building. I would like to know if there are javadocs for the JMOL Viewer Classes. I have tried searching the Web, but I haven`t found enough material. I would be very greatful if you could help me. Thank you very much Nkemdilim Uwaje -- GMX im TV ... Die Gedanken sind frei ... Schon gesehen? Jetzt Spot online ansehen: http://www.gmx.net/de/go/tv-spot |
From: Bharath R. <bha...@ms...> - 2005-04-04 07:04:02
|
hello, i am in requirement of Jmol API specification/documentation and i would also like to ask Mr.Miguel if you could please provide me the script that the applet runs on JMol homepage? as i would like to know how the text display is possible thank you, Bharath Reddy, 1203ab001, MSIT 2003, International Institute of Information Technology. |
From: Egon W. <eg...@us...> - 2005-04-04 07:13:58
|
On Monday 4 April 2005 14:29, Bharath Reddy wrote: > i am in requirement of Jmol API specification/documentation and i would > also like to ask Mr.Miguel if you could please provide me the script that > the applet runs on JMol homepage? Our Jmol is with a lower case 'm'... another rendering applet is with a upper case M... > as i would like to know how the text display is possible The source can be found in CVS, in the Jmol-web module in the source/doc/script subdirectory. A snippet of the script: load model/jmol.mol.gz; set frank off; spacefill off; wireframe off; set echo top center; font echo 22 serif; color echo white echo "The future ..." delay 3 set echo middle center; font echo 22 serif; color echo white echo "of molecular visualization" delay 3 set echo bottom center; font echo 22 serif; color echo white echo "... has arrived ..." delay 5 # set echo off; set echo middle center; font echo 60 serif bold; color echo yellow echo "Jmol" delay 2 set echo off; color atoms gold; color bonds yellow zoom 10; wireframe .25; spacefill .3; moveto 1 0 0 0 0 140; delay 2; moveTo 1 5 345 939 79.5 24 51 57 script script/smallMolecules.en.txt set echo off; restrict none; set echo off; set echo top center; font echo 22; color echo cyan echo "This is *not* a movie ..." delay 2; set echo middle center; font echo 30; color echo tomato echo "... this is reality ..." delay 2; set echo bottom center; font echo 22; color echo lime echo "virtual reality for molecules" delay 3; # set echo off; set echo middle center; font echo 60 serif bold; color echo yellow echo "Jmol" delay 4 Egon -- eg...@us... GPG: 1024D/D6336BA6 |
From: Geoff H. <ge...@ge...> - 2005-06-02 01:29:41
|
I'm happy to announce the release of the first public snapshot of the Open Babel test file repository 2005-06-01. This repository is an open resource for the purposes of test molecules, scripts and results in various chemical file formats. Releases are expected several times a year. The test set includes 39 "canonical" files (including 20 formats) and 47 additional files. Many file formats have formal specifications (e.g., CML or PDB) but realistically, such specifications evolve, many files are passed around which do not adhere to these specifications, and without example reference files, the details of file format specifications are not always clear. Importantly these files can be used for testing import/export routines in many chemical programs, not just Open Babel. By providing such a resource, we hope that developers of chemical software will minimize bugs when translating chemical and molecular data between different file formats and different representations. Additionally, we hope to encourage the community of chemical software developers to support open, well-defined file formats to facilitate interconversion and collaboration in the chemical sciences. * For more information, check: <http://openbabel.sourceforge.net/ repository/> * To download the release: <http://sourceforge.net/project/ showfiles.php?group_id=40728&package_id=152710> * To discuss the release (ope...@li...): <http://sourceforge.net/mailarchive/forum.php?forum_id=45088> Please consider contributing files: http://sourceforge.net/tracker/? atid=740158&group_id=40728&func=browse Cheers, -Geoff (Please distribute this announcement as you see fit to chemistry/ cheminformtics software developers, etc.) |
From: Dan G. <gez...@nd...> - 2006-06-13 17:28:45
|
Greetings, Jmol team! I've become interested (for various reasons) in displaying non-spherical atoms in Jmol. One possible application would be to show thermal ellipsoids (i.e. to generate ORTEP-style plots from x-ray data). The application I have in mind for ellipsoids is to display atoms from a Gay-Berne simulation (the Gay-Berne potential is an ellipsoidal generalization of Lennard-Jones that has become common in the liquid crystal community. Right now, we're using atom-associated vectors for visualization within Jmol, and have modified the PovraySaver to construct ellipsoids from the atom positions and the vectors. In your estimation, how difficult would it be to modify the classes in g3d to render an ellipsoid within Jmol itself? In Povray, an ellipsoid is simply a stretched (or squashed) sphere that is then rotated and translated into the correct position. I imagine this is somewhat more difficult in the g3d rendering scheme. Any ideas if this is a feasible? Best regards, --Dan *********************************************** J. Daniel Gezelter Associate Professor Department of Chemistry and Biochemistry 251 Nieuwland Science Hall University of Notre Dame Notre Dame, IN 46556-5670 phone: +1 (574) 631-7595 fax: +1 (574) 631-6652 e-mail: gez...@nd... web: http://www.nd.edu/~gezelter ************************************************ |
From: Miguel <mi...@jm...> - 2006-06-14 01:08:07
|
> Greetings, Jmol team=21 > > I've become interested (for various reasons) in displaying > non-spherical atoms in Jmol. One possible application would > be to show thermal ellipsoids (i.e. to generate ORTEP-style plots > from x-ray data). The application I have in mind for ellipsoids > is to display atoms from a Gay-Berne simulation (the Gay-Berne potentia= l > is an ellipsoidal generalization of Lennard-Jones that has become > common in the liquid crystal community. A few years ago someone asked about displaying ORTEP ellipsoids. > Right now, we're using atom-associated vectors for visualization > within Jmol, and have modified the PovraySaver to construct > ellipsoids from the atom positions and the vectors. > > In your estimation, how difficult would it be to modify the classes > in g3d to render an ellipsoid within Jmol itself? Unfortunately, I think that it would be rather difficult. The beauty of a sphere is that it looks the same from every direction. That means that shape & shading information can be precalculated and cached, allowing relatively high performance rendering. An ellipsoid changes shape depending upon the viewing angle. Therefore, different techniques would need to be used. > In Povray, an > ellipsoid is simply a stretched (or squashed) sphere that is then > rotated and translated into the correct position. I imagine this is > somewhat more difficult in the g3d rendering scheme. Correct. > Any ideas if this is a feasible? It could be done ... but I don't think it would be easy. Some questions: It will be much more expensive than rendering a sphere. But, that may not= be a problem if we are rendering relatively few ellipsoids ... Q: Do people want to render proteins with thousands of ellipsoids? Or is this generally applied to smaller molecules (or small portions of proteins)? Make a wild guess at completing the following sentences: Most molecules would have ---- ellipsoids. The largest reasonable molecule would have ---- ellipsoids. Q: Are all the ellipsoids the same shape, just scaled to different sizes?= Or are some of them more elongated than others? Q: Within a given molecule, are there usually multiple ellipsoids that ar= e the same size & shape? Miguel |
From: Bob H. <ha...@st...> - 2006-06-14 02:39:56
|
The simplest way of implementing ellipsoids just might be with isosurfaces. All one needs is the surface for a simple sphere, but because we have vectors that define x, y, and z, independently scalable, those would handle all the distortion needed. If it were considered like an orbital, then perhaps the two solutions will converge -- both require centering, scaling, and (even in the case of orbitals, depending upon one's aesthetics) possible stretching. The remaining piece would be orienting the ellipsoid properly. We could even provide the ortep-like quarter-ellipse cutout if desired. Q: How are these anisotropic parameters generally described? Does each atom just require three vectors that describe its ellipse? I might play with this a bit. Bob Miguel wrote: >>Greetings, Jmol team! >> >> I've become interested (for various reasons) in displaying >>non-spherical atoms in Jmol. One possible application would >>be to show thermal ellipsoids (i.e. to generate ORTEP-style plots >>from x-ray data). The application I have in mind for ellipsoids >>is to display atoms from a Gay-Berne simulation (the Gay-Berne potential >>is an ellipsoidal generalization of Lennard-Jones that has become >>common in the liquid crystal community. >> >> > >A few years ago someone asked about displaying ORTEP ellipsoids. > > > >>Right now, we're using atom-associated vectors for visualization >>within Jmol, and have modified the PovraySaver to construct >>ellipsoids from the atom positions and the vectors. >> >>In your estimation, how difficult would it be to modify the classes >>in g3d to render an ellipsoid within Jmol itself? >> >> > >Unfortunately, I think that it would be rather difficult. > >The beauty of a sphere is that it looks the same from every direction. >That means that shape & shading information can be precalculated and >cached, allowing relatively high performance rendering. > >An ellipsoid changes shape depending upon the viewing angle. Therefore, >different techniques would need to be used. > > > >>In Povray, an >>ellipsoid is simply a stretched (or squashed) sphere that is then >>rotated and translated into the correct position. I imagine this is >>somewhat more difficult in the g3d rendering scheme. >> >> > >Correct. > > > >>Any ideas if this is a feasible? >> >> > >It could be done ... but I don't think it would be easy. > >Some questions: > >It will be much more expensive than rendering a sphere. But, that may not >be a problem if we are rendering relatively few ellipsoids ... > >Q: Do people want to render proteins with thousands of ellipsoids? Or is >this generally applied to smaller molecules (or small portions of >proteins)? > >Make a wild guess at completing the following sentences: > >Most molecules would have ---- ellipsoids. > >The largest reasonable molecule would have ---- ellipsoids. > >Q: Are all the ellipsoids the same shape, just scaled to different sizes? >Or are some of them more elongated than others? > >Q: Within a given molecule, are there usually multiple ellipsoids that are >the same size & shape? > > > >Miguel > > > >_______________________________________________ >Jmol-developers mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > |
From: Bob H. <ha...@st...> - 2006-06-14 03:18:51
|
addendum. See http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm command: isosurface center {x y z} anisotropy {a b c} orbital 1 0 0 2; for discussion. Hokey way to make a sphere, but, hey, it works! Bob Bob Hanson wrote: >The simplest way of implementing ellipsoids just might be with >isosurfaces. All one needs is the surface for a simple sphere, but >because we have vectors that define x, y, and z, independently scalable, >those would handle all the distortion needed. If it were considered like >an orbital, then perhaps the two solutions will converge -- both require >centering, scaling, and (even in the case of orbitals, depending upon >one's aesthetics) possible stretching. The remaining piece would be >orienting the ellipsoid properly. We could even provide the ortep-like >quarter-ellipse cutout if desired. > >Q: How are these anisotropic parameters generally described? Does each >atom just require three vectors that describe its ellipse? > >I might play with this a bit. > >Bob > > > >Miguel wrote: > > > >>>Greetings, Jmol team! >>> >>> I've become interested (for various reasons) in displaying >>>non-spherical atoms in Jmol. One possible application would >>>be to show thermal ellipsoids (i.e. to generate ORTEP-style plots >>> >>> >>>from x-ray data). The application I have in mind for ellipsoids >> >> >>>is to display atoms from a Gay-Berne simulation (the Gay-Berne potential >>>is an ellipsoidal generalization of Lennard-Jones that has become >>>common in the liquid crystal community. >>> >>> >>> >>> >>A few years ago someone asked about displaying ORTEP ellipsoids. >> >> >> >> >> >>>Right now, we're using atom-associated vectors for visualization >>>within Jmol, and have modified the PovraySaver to construct >>>ellipsoids from the atom positions and the vectors. >>> >>>In your estimation, how difficult would it be to modify the classes >>>in g3d to render an ellipsoid within Jmol itself? >>> >>> >>> >>> >>Unfortunately, I think that it would be rather difficult. >> >>The beauty of a sphere is that it looks the same from every direction. >>That means that shape & shading information can be precalculated and >>cached, allowing relatively high performance rendering. >> >>An ellipsoid changes shape depending upon the viewing angle. Therefore, >>different techniques would need to be used. >> >> >> >> >> >>>In Povray, an >>>ellipsoid is simply a stretched (or squashed) sphere that is then >>>rotated and translated into the correct position. I imagine this is >>>somewhat more difficult in the g3d rendering scheme. >>> >>> >>> >>> >>Correct. >> >> >> >> >> >>>Any ideas if this is a feasible? >>> >>> >>> >>> >>It could be done ... but I don't think it would be easy. >> >>Some questions: >> >>It will be much more expensive than rendering a sphere. But, that may not >>be a problem if we are rendering relatively few ellipsoids ... >> >>Q: Do people want to render proteins with thousands of ellipsoids? Or is >>this generally applied to smaller molecules (or small portions of >>proteins)? >> >>Make a wild guess at completing the following sentences: >> >>Most molecules would have ---- ellipsoids. >> >>The largest reasonable molecule would have ---- ellipsoids. >> >>Q: Are all the ellipsoids the same shape, just scaled to different sizes? >>Or are some of them more elongated than others? >> >>Q: Within a given molecule, are there usually multiple ellipsoids that are >>the same size & shape? >> >> >> >>Miguel >> >> >> >>_______________________________________________ >>Jmol-developers mailing list >>Jmo...@li... >>https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> >> >> > > > >_______________________________________________ >Jmol-developers mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > |
From: Emily H. <em...@bu...> - 2008-02-13 22:03:05
|
Hi, I am looking at the contents of a pdb file. Can someone tell me how/if the single-letter residue sequence is contained in that file? Emily Emily Heureux Software Developer Laboratory of Professor Jeffrey W. Smith, Ph.D. Director, Center on Proteolytic Pathways Director, Program for Excellence in Nanotechnology BURNHAM INSTITUTE for Medical Research 10901 North Torrey Pines Road La Jolla, California 92037 T | 858.646.3100 x 4013 F | 858.795.5221 www.burnham.org This communication and any attached documents are for the intended recipient(s) only, and may contain information that is protected by legal privilege, confidential and exempt from disclosure under applicable law. If you are not the intended recipient or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any unauthorized use, disclosure, dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately by telephone (858.646.3100) or e-mail reply, delete it from your system, and destroy any hard copy you may have printed. Thank you for your cooperation. |
From: A. H. <ang...@ua...> - 2008-02-13 22:26:03
|
I'm afraid not, Emily You should have the three-letter sequence, divided up along several lines, marked "SEQRES" at the beginning. That's for proteins, of course. Nucleic acids do use a one-letter system. > Hi, I am looking at the contents of a pdb file. Can someone tell me how/if the single-letter > residue sequence is contained in that file? |
From: Kirby S. <kir...@gm...> - 2008-02-14 00:21:32
|
The PDB formats are described here: http://www.wwpdb.org/documentation/format23/v2.3.html http://www.wwpdb.org/documentation/format30/ You should also be aware of MODRES (modified residue) in addition to SEQRES records. On Feb 13, 2008 2:36 PM, Angel Herráez <ang...@ua...> wrote: > I'm afraid not, Emily > You should have the three-letter sequence, divided up along several lines, > marked > "SEQRES" at the beginning. > > That's for proteins, of course. Nucleic acids do use a one-letter system. > > > Hi, I am looking at the contents of a pdb file. Can someone tell me > how/if the single-letter > > residue sequence is contained in that file? > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > |
From: Rolf H. <rh...@fl...> - 2008-02-14 11:24:20
|
Angel Herráez wrote: > I'm afraid not, Emily > You should have the three-letter sequence, divided up along several lines, marked > "SEQRES" at the beginning. > > That's for proteins, of course. Nucleic acids do use a one-letter system. > That was before the remediation of the PDB files (for standard nucleic acids). Since the remediation the standard DNA residues have a two-letter code (e.g.: DA,DC,DG,DT) while the standard RNA residues have a one-letter code (e.g.: A,C,G,U). Modified nucleic acids where marked before the remediation with a "+" sign (e.g.: +A,+C). Since the remediation they have individual three-letter codes which are defined in the "HET" records of the PDB file. Regards, Rolf |
From: j b. k. <jbr...@gm...> - 2008-05-19 03:04:56
|
Hi, I'm new to Jmol. I'm trying to run it via Java Web start. Even doing a simple jnlp like that below *doesn't work*. I click on the link and the Java logo comes up but then *nothing happens*. What basic thing am I doing wrong. <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" codebase="http://trueblue.caltech.edu/java"> <information> <title>Jmol</title> <vendor>DANSE</vendor> <homepage href="http://danse.us" /> <description>Jmol</description> </information> <offline-allowed/> <security> <all-permissions/> </security> <resources> <j2se version="1.5+" /> <jar href="Jmol.jar" /> </resources> <component-desc main-class="org.openscience.jmol.app.Jmol" /> </jnlp> I'm using Java 6. It works fine from the command line: java -jar Jmol.jar Also, I'd like to launch Jmol via Java web start (jws) and have it automatically load a cif file. However, I believe jws cannot accept parameters. So I write a class that calls jmol and loads "sample.cif" from a dynamically generated code base: <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" codebase="http://trueblue.caltech.edu/java"> <information> <title>Sample Viewer</title> <vendor>DANSE</vendor> <homepage href="http://danse.us" /> <description>Sample Viewer</description> </information> <offline-allowed/> <security> <all-permissions/> </security> <resources> <j2se version="1.5+" java-vm-args="-Xmx512m -splash:splash.png"/> <jar href="sampleViewer.jar"/> <jar href="Jmol.jar" /> </resources> <component-desc main-class="sampleViewer.Main" /> </jnlp> But that doesn't work either (probably related to previous error). But is this the best way to do this or is there a javascript way that is better? PS: Don't want to use just applets--need jws to work as well. -- J. Brandon Keith |
From: Herráez S. A. <ang...@ua...> - 2008-05-20 12:00:02
|
Hi Brandon I hacve no experience with JWS, but have you read the section in the Wiki? http://wiki.jmol.org:81/index.php/Java_Web_Start ________________________________ De: jmo...@li... em nome de j brandon keith Enviada: seg 19/05/2008 5:04 Para: jmo...@li... Assunto: [Jmol-developers] (no subject) Hi, I'm new to Jmol. I'm trying to run it via Java Web start. Even doing a simple jnlp like that below *doesn't work*. I click on the link and the Java logo comes up but then *nothing happens*. What basic thing am I doing wrong. <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" codebase="http://trueblue.caltech.edu/java"> <information> <title>Jmol</title> <vendor>DANSE</vendor> <homepage href="http://danse.us <http://danse.us/> " /> <description>Jmol</description> </information> <offline-allowed/> <security> <all-permissions/> </security> <resources> <j2se version="1.5+" /> <jar href="Jmol.jar" /> </resources> <component-desc main-class="org.openscience.jmol.app.Jmol" /> </jnlp> I'm using Java 6. It works fine from the command line: java -jar Jmol.jar Also, I'd like to launch Jmol via Java web start (jws) and have it automatically load a cif file. However, I believe jws cannot accept parameters. So I write a class that calls jmol and loads "sample.cif" from a dynamically generated code base: <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" codebase="http://trueblue.caltech.edu/java"> <information> <title>Sample Viewer</title> <vendor>DANSE</vendor> <homepage href="http://danse.us <http://danse.us/> " /> <description>Sample Viewer</description> </information> <offline-allowed/> <security> <all-permissions/> </security> <resources> <j2se version="1.5+" java-vm-args="-Xmx512m -splash:splash.png"/> <jar href="sampleViewer.jar"/> <jar href="Jmol.jar" /> </resources> <component-desc main-class="sampleViewer.Main" /> </jnlp> But that doesn't work either (probably related to previous error). But is this the best way to do this or is there a javascript way that is better? PS: Don't want to use just applets--need jws to work as well. -- J. Brandon Keith ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-developers mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-developers |
From: Bob H. <ha...@st...> - 2008-05-20 14:18:23
|
Brandon, the following cobbled-together code worked for me. The file was c:\temp\t2.jnlp, and Jmol.jar was in c:\temp as well. So maybe it's just the "application-desc" instead of "component-desc" Not sure how you send commandline options. Bob <?xml version="1.0" encoding="utf-8"?> <jnlp spec="0.2 1.0" codebase="file:///c:/temp" href="t2.jnlp"> <information> <title>SwingSet2 App</title> <vendor>Sun Microsystems, Inc.</vendor> <homepage href="http://java.sun.com/products/javawebstart/demos.html"/> <description>SwingSet2 Demo Description</description> <description kind="short">SwingSet2 Demo Short Description</description> <offline-allowed/> </information> <security> <all-permissions/> </security> <resources> <j2se version="1.3+" href="http://java.sun.com/products/autodl/j2se"/> <j2se version="1.3+"/> <jar href="Jmol.jar" main="true" download="eager"/> </resources> <application-desc main-class="org.openscience.jmol.app.Jmol"/> </jnlp> Bob Hanson j brandon keith wrote: >Hi, I'm new to Jmol. I'm trying to run it via Java Web start. Even >doing a simple jnlp like that below *doesn't work*. I click on the >link and the Java logo comes up but then *nothing happens*. What >basic thing am I doing wrong. > ><?xml version="1.0" encoding="UTF-8"?> ><jnlp spec="1.0+" > codebase="http://trueblue.caltech.edu/java"> > <information> > <title>Jmol</title> > <vendor>DANSE</vendor> > <homepage href="http://danse.us" /> > <description>Jmol</description> > </information> > <offline-allowed/> > <security> > <all-permissions/> > </security> > <resources> > <j2se version="1.5+" /> > <jar href="Jmol.jar" /> > </resources> > <component-desc main-class="org.openscience.jmol.app.Jmol" /> ></jnlp> > >I'm using Java 6. It works fine from the command line: java -jar Jmol.jar > >Also, I'd like to launch Jmol via Java web start (jws) and have it >automatically load a cif file. However, I believe jws cannot accept >parameters. So I write a class that calls jmol and loads "sample.cif" >from a dynamically generated code base: > > <?xml version="1.0" encoding="UTF-8"?> ><jnlp spec="1.0+" > codebase="http://trueblue.caltech.edu/java"> > <information> > <title>Sample Viewer</title> > <vendor>DANSE</vendor> > <homepage href="http://danse.us" /> > <description>Sample Viewer</description> > </information> > <offline-allowed/> > <security> > <all-permissions/> > </security> > <resources> > <j2se version="1.5+" java-vm-args="-Xmx512m -splash:splash.png"/> > <jar href="sampleViewer.jar"/> > <jar href="Jmol.jar" /> > </resources> > <component-desc main-class="sampleViewer.Main" /> ></jnlp> > >But that doesn't work either (probably related to previous error). >But is this the best way to do this or is there a javascript way that >is better? > >PS: Don't want to use just applets--need jws to work as well. > > > -- 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 XXX, Monday, February 5, 1900 |
From: Rolf H. <rh...@fl...> - 2008-05-20 14:50:45
|
j brandon keith wrote: > Hi, I'm new to Jmol. I'm trying to run it via Java Web start. Even > doing a simple jnlp like that below *doesn't work*. I click on the > link and the Java logo comes up but then *nothing happens*. What > basic thing am I doing wrong. > > <?xml version="1.0" encoding="UTF-8"?> > <jnlp spec="1.0+" > codebase="http://trueblue.caltech.edu/java"> > <information> > <title>Jmol</title> > <vendor>DANSE</vendor> > <homepage href="http://danse.us" /> > <description>Jmol</description> > </information> > <offline-allowed/> > <security> > <all-permissions/> > </security> > <resources> > <j2se version="1.5+" /> > <jar href="Jmol.jar" /> > </resources> > <component-desc main-class="org.openscience.jmol.app.Jmol" /> > </jnlp> > > I'm using Java 6. It works fine from the command line: java -jar Jmol.jar > > Also, I'd like to launch Jmol via Java web start (jws) and have it > automatically load a cif file. However, I believe jws cannot accept > parameters. So I write a class that calls jmol and loads "sample.cif" > from a dynamically generated code base: > > <?xml version="1.0" encoding="UTF-8"?> > <jnlp spec="1.0+" > codebase="http://trueblue.caltech.edu/java"> > <information> > <title>Sample Viewer</title> > <vendor>DANSE</vendor> > <homepage href="http://danse.us" /> > <description>Sample Viewer</description> > </information> > <offline-allowed/> > <security> > <all-permissions/> > </security> > <resources> > <j2se version="1.5+" java-vm-args="-Xmx512m -splash:splash.png"/> > <jar href="sampleViewer.jar"/> > <jar href="Jmol.jar" /> > </resources> > <component-desc main-class="sampleViewer.Main" /> > </jnlp> > > But that doesn't work either (probably related to previous error). > But is this the best way to do this or is there a javascript way that > is better? > I have no experience with configuring Java web start applications. But from a brief look at the start process of existing web start applications I would suggest the following: 1) If it is sufficient to have fixed arguments just integrate something like this into your 'jnlp' file: <application-desc main-class="org.openscience.jmol.app.Jmol"> <argument>-s default.script</argument> <argument>sample.cif</argument> </application-desc> 2) If there are dynamic arguments then you could write a little CGI script (PHP, Perl, etc.) that returns a customized 'jnlp' file. Regards, Rolf |
From: Jeroen L. <jer...@ho...> - 2009-02-12 15:28:26
|
Hello! I'm trying to convince the Jmol standalone application to load a custom menu using the 'load menu' script. However, this generates the following exception: Disposal was interrupted: java.lang.InterruptedException at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:485) at java.awt.EventQueue.invokeAndWait(Unknown Source) at java.awt.Window.doDispose(Unknown Source) at java.awt.Window.dispose(Unknown Source) at org.openscience.jmol.app.Jmol.dispose(Unknown Source) at org.openscience.jmol.app.Jmol.setupNewFrame(Unknown Source) at org.openscience.jmol.app.Jmol$MyStatusListener.setCallbackFunction(Unknown Source) at org.jmol.viewer.StatusManager.setCallbackFunction(Unknown Source) at org.jmol.viewer.Viewer.setMenu(Unknown Source) at org.jmol.viewer.Eval.load(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.runEval(Unknown Source) at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source) at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown Source) at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Even when loading the default menu (dumped with the 'write menu' script), this exception occurs. I've tried using different versions (11.7.25, 11.6.15, 11.4.6, even 11.2.14). I'm starting the application using org.openscience.jmol.app.getJmol.getJmol(...). Is it a bug or is there something that I'm doing wrong? thanks in advance, Jeroen _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
From: Robert H. <ha...@st...> - 2009-02-12 16:10:56
|
Yes, I get that, too. As far as I can tell it's harmless -- the menu is loaded, and Jmol continues past the exception. Could be a Java bug. -- Right? I can see the code: try { f.dispose(); if (scriptWindow != null) { scriptWindow.dispose(); } } catch (Exception e) { // ignore } Oddly enough the message is displayed upon execution of f.dispose(), but Jmol continues on to the scriptWindowDispose() anyway, as though no exception were thrown (which is fine). Bob On Thu, Feb 12, 2009 at 9:28 AM, Jeroen Logtenberg < jer...@ho...> wrote: > Hello! > > I'm trying to convince the Jmol standalone application to load a custom > menu using the 'load menu' script. However, this generates the following > exception: > > Disposal was interrupted: > java.lang.InterruptedException > at java.lang.Object.wait(Native Method) > at java.lang.Object.wait(Object.java:485) > at java.awt.EventQueue.invokeAndWait(Unknown Source) > at java.awt.Window.doDispose(Unknown Source) > at java.awt.Window.dispose(Unknown Source) > at org.openscience.jmol.app.Jmol.dispose(Unknown Source) > at org.openscience.jmol.app.Jmol.setupNewFrame(Unknown Source) > at > org.openscience.jmol.app.Jmol$MyStatusListener.setCallbackFunction(Unknown > Source) > at org.jmol.viewer.StatusManager.setCallbackFunction(Unknown > Source) > at org.jmol.viewer.Viewer.setMenu(Unknown Source) > at org.jmol.viewer.Eval.load(Unknown Source) > at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) > at org.jmol.viewer.Eval.runEval(Unknown Source) > at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) > at > org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source) > at > org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown > Source) > at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown > Source) > at java.lang.Thread.run(Unknown Source) > > Even when loading the default menu (dumped with the 'write menu' script), > this exception occurs. I've tried using different versions (11.7.25, > 11.6.15, 11.4.6, even 11.2.14). I'm starting the application using > org.openscience.jmol.app.getJmol.getJmol(...). > > Is it a bug or is there something that I'm doing wrong? > > thanks in advance, > Jeroen > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > ------------------------------------------------------------------------------ > Create and Deploy Rich Internet Apps outside the browser with > Adobe(R)AIR(TM) > software. With Adobe AIR, Ajax developers can use existing skills and code > to > build responsive, highly engaging applications that combine the power of > local > resources and data with the reach of the web. Download the Adobe AIR SDK > and > Ajax docs to start building applications today- > http://p.sf.net/sfu/adobe-com > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Angel H. <ang...@ua...> - 2009-02-12 16:11:38
|
Hello Jeroen > Even when loading the default menu (dumped with the 'write menu' > script), this exception occurs. I've tried using different versions > (11.7.25, 11.6.15, 11.4.6, even 11.2.14). There has been a bug across several later versions. This was found recently and fixed in 11.6.13 and 11.7.21 The feature was introduced in 11.3.15, so - 11.2 will not work - 11.4 may or not work - 11.6.15 and 11.7.25 should be OK > I'm starting the > application using org.openscience.jmol.app.getJmol.getJmol(...). I don't understand this method. Please try first to execute the Jmol.jar file and see what happens. Others may help you with that, but first let's make sure if the normal use of the app works or not. The scripted "load menu" method is documented only for the applet; I'd expect it to work in the app too, but haven't tried that yet. This works for me in 11.6.16: java -jar Jmol.jar -m test.mnu And this works too: java -jar Jmol.jar load menu "text.mnu" # (entered in the script console) |
From: Jeroen L. <jer...@ho...> - 2009-02-12 16:26:29
|
> From: ang...@ua... > To: jmo...@li... > Date: Thu, 12 Feb 2009 17:14:46 +0100 > Subject: Re: [Jmol-developers] Loading custom menus [was (no subject)] > > Hello Jeroen > > > Even when loading the default menu (dumped with the 'write menu' > > script), this exception occurs. I've tried using different versions > > (11.7.25, 11.6.15, 11.4.6, even 11.2.14). > > There has been a bug across several later versions. This was found > recently and fixed in 11.6.13 and 11.7.21 > > The feature was introduced in 11.3.15, so > - 11.2 will not work > - 11.4 may or not work > - 11.6.15 and 11.7.25 should be OK > > > > I'm starting the > > application using org.openscience.jmol.app.getJmol.getJmol(...). > > I don't understand this method. Please try first to execute the > Jmol.jar file and see what happens. Others may help you with that, > but first let's make sure if the normal use of the app works or not. > > The scripted "load menu" method is documented only for the applet; > I'd expect it to work in the app too, but haven't tried that yet. > > This works for me in 11.6.16: > java -jar Jmol.jar -m test.mnu > > And this works too: > java -jar Jmol.jar > load menu "text.mnu" # (entered in the script console) I've tried these options as well, the problem remains the same. The reason that I use the strange way of opening is because I launch jmol from another java program. _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
From: Jeroen L. <jer...@ho...> - 2009-02-12 16:32:30
|
I thought it was harmless at first too, but I'm having problems getting script commands to work after the exception. My java code says for example: m_JmolApp.viewer.evalString("load MENU custom.mnu"); m_JmolApp.viewer.evalString("set picking CENTER"); The menu loads like it's supposed to, but the center picking refuses to activate. Jeroen Date: Thu, 12 Feb 2009 10:10:52 -0600 From: ha...@st... To: jmo...@li... Subject: Re: [Jmol-developers] (no subject) Yes, I get that, too. As far as I can tell it's harmless -- the menu is loaded, and Jmol continues past the exception. Could be a Java bug. -- Right? I can see the code: try { f.dispose(); if (scriptWindow != null) { scriptWindow.dispose(); } } catch (Exception e) { // ignore } Oddly enough the message is displayed upon execution of f.dispose(), but Jmol continues on to the scriptWindowDispose() anyway, as though no exception were thrown (which is fine). Bob On Thu, Feb 12, 2009 at 9:28 AM, Jeroen Logtenberg <jer...@ho...> wrote: Hello! I'm trying to convince the Jmol standalone application to load a custom menu using the 'load menu' script. However, this generates the following exception: Disposal was interrupted: java.lang.InterruptedException at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:485) at java.awt.EventQueue.invokeAndWait(Unknown Source) at java.awt.Window.doDispose(Unknown Source) at java.awt.Window.dispose(Unknown Source) at org.openscience.jmol.app.Jmol.dispose(Unknown Source) at org.openscience.jmol.app.Jmol.setupNewFrame(Unknown Source) at org.openscience.jmol.app.Jmol$MyStatusListener.setCallbackFunction(Unknown Source) at org.jmol.viewer.StatusManager.setCallbackFunction(Unknown Source) at org.jmol.viewer.Viewer.setMenu(Unknown Source) at org.jmol.viewer.Eval.load(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.runEval(Unknown Source) at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source) at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown Source) at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Even when loading the default menu (dumped with the 'write menu' script), this exception occurs. I've tried using different versions (11.7.25, 11.6.15, 11.4.6, even 11.2.14). I'm starting the application using org.openscience.jmol.app.getJmol.getJmol(...). Is it a bug or is there something that I'm doing wrong? thanks in advance, Jeroen Express yourself instantly with MSN Messenger! MSN Messenger ------------------------------------------------------------------------------ Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com _______________________________________________ Jmol-developers mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 _________________________________________________________________ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx |
From: Robert H. <ha...@st...> - 2009-02-13 06:06:44
|
Oh, I see. What you don't realize is that a whole new viewer is created. I'm not sure where your m_JmolApp.viewer comes from, but whatever it is, it won't do anything after the load MENU command. public void setCallbackFunction(String callbackType, String callbackFunction) { if (callbackType.equalsIgnoreCase("menu")) { menuStructure = callbackFunction; menuFile = null; setupNewFrame(viewer.getStateInfo()); return; } ... } protected void setupNewFrame(String state) { JFrame newFrame = new JFrame(); JFrame f = this.frame; Jmol j = new Jmol(null, newFrame, Jmol.this, startupWidth, startupHeight, "", (state == null ? null : f.getLocationOnScreen())); newFrame.show(); if (state != null) { dispose(f); j.viewer.evalStringQuiet(state); } } Are you perhaps doing this from Jmol in an embedded application, not the Jmol applet itself? If so, what does YOUR setCallbackFunction() do? Notice that in setupNewFrame() we create a completely new instance of Jmol and load the previous state. That new instance has a new viewer. That's what is causing you the problem. You are using the wrong viewer. I don't think you can string the commands together like that. Basically, the language changing isn't generally applicable without some pretty tricky coding. Bob 2009/2/12 Jeroen Logtenberg <jer...@ho...> > I thought it was harmless at first too, but I'm having problems getting > script commands to work after the exception. My java code says for example: > m_JmolApp.viewer.evalString("load MENU custom.mnu"); > m_JmolApp.viewer.evalString("set picking CENTER"); > > The menu loads like it's supposed to, but the center picking refuses to > activate. > > Jeroen > > ------------------------------ > Date: Thu, 12 Feb 2009 10:10:52 -0600 > From: ha...@st... > To: jmo...@li... > Subject: Re: [Jmol-developers] (no subject) > > Yes, I get that, too. As far as I can tell it's harmless -- the menu is > loaded, and Jmol continues past the exception. Could be a Java bug. -- > Right? I can see the code: > > try { > f.dispose(); > if (scriptWindow != null) { > scriptWindow.dispose(); > } > } catch (Exception e) { > // ignore > } > > Oddly enough the message is displayed upon execution of f.dispose(), but > Jmol continues on to the scriptWindowDispose() anyway, as though no > exception were thrown (which is fine). > > Bob > > > On Thu, Feb 12, 2009 at 9:28 AM, Jeroen Logtenberg < > jer...@ho...> wrote: > > Hello! > > I'm trying to convince the Jmol standalone application to load a custom > menu using the 'load menu' script. However, this generates the following > exception: > > Disposal was interrupted: > java.lang.InterruptedException > at java.lang.Object.wait(Native Method) > at java.lang.Object.wait(Object.java:485) > at java.awt.EventQueue.invokeAndWait(Unknown Source) > at java.awt.Window.doDispose(Unknown Source) > at java.awt.Window.dispose(Unknown Source) > at org.openscience.jmol.app.Jmol.dispose(Unknown Source) > at org.openscience.jmol.app.Jmol.setupNewFrame(Unknown Source) > at > org.openscience.jmol.app.Jmol$MyStatusListener.setCallbackFunction(Unknown > Source) > at org.jmol.viewer.StatusManager.setCallbackFunction(Unknown > Source) > at org.jmol.viewer.Viewer.setMenu(Unknown Source) > at org.jmol.viewer.Eval.load(Unknown Source) > at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) > at org.jmol.viewer.Eval.runEval(Unknown Source) > at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) > at > org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source) > at > org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown > Source) > at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown > Source) > at java.lang.Thread.run(Unknown Source) > > Even when loading the default menu (dumped with the 'write menu' script), > this exception occurs. I've tried using different versions (11.7.25, > 11.6.15, 11.4.6, even 11.2.14). I'm starting the application using > org.openscience.jmol.app.getJmol.getJmol(...). > > Is it a bug or is there something that I'm doing wrong? > > thanks in advance, > Jeroen > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > ------------------------------------------------------------------------------ > Create and Deploy Rich Internet Apps outside the browser with > Adobe(R)AIR(TM) > software. With Adobe AIR, Ajax developers can use existing skills and code > to > build responsive, highly engaging applications that combine the power of > local > resources and data with the reach of the web. Download the Adobe AIR SDK > and > Ajax docs to start building applications today- > http://p.sf.net/sfu/adobe-com > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > ------------------------------ > See all the ways you can stay connected to friends and family<http://www.microsoft.com/windows/windowslive/default.aspx> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: P.Canepa <pc...@ke...> - 2010-02-16 19:12:59
|
Dear Bob, have you got my e-mail along with some example of crystal outputs? Thanks, Piero -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@ke... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- |
From: P.Canepa <pc...@ke...> - 2010-02-17 14:08:57
|
Dear Bob, have you got my e-mail along with some example of crystal outputs? I saw Jmol can deal with the optimization of gaussian Structure! Which class is doing it, I would like to implement it for CRYSTAL, since now I can open the structure correctly! Futhermore there is any class which exploit the symmetry of the crystal in Jmol? It is compatible with the 230 space groups defined into the international tables for crystallographers? Does this read Space Groups express with the Hermann-Mauguin notation? Thanks, Piero -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@ke... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- |
From: Egon W. <eg...@us...> - 2005-01-26 13:34:54
|
On Wednesday 26 January 2005 11:42, Nkemdilim Uwaje wrote: > My name is Nkemdilim Uwaje and I am a bioinformatics student at the LMU in > Munich and I am trying to develop a graphic user interface (using Java) for > a chemical library that I am building. I would like to know if there are > javadocs for the JMOL Viewer Classes. I have tried searching the Web, but I > haven`t found enough material. I would be very greatful if you could help > me. JavaDoc is rather limited at this moment, but there is some documentation at: http://wiki.jmol.org/ApplicationsEmbeddingJmol Egon -- eg...@us... GPG: 1024D/D6336BA6 |