[Jmol-users] Really Ugly Windows Firefox Issue
All, My Firefox on Window 7 just updated to 3.6.14. After the update, I started seeing intermittent Jmol applet corruption. This can be initiated with a page reload. I noticed it first on a page I was working on, but I also checked it on this page: http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model= data/cyclohexaneFlip.jmol And this page: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Two reloads corrupted the applet on both pages. Once corrupted, you have to quit Firefox and restart to load the applet again. I've attached the Java Console reports for these cases at the end of this email. I am using an older version of Java. This is because recent Java updates have a security problem with local host development. Oracle is aware of the local host problem, but they essentially say too bad! Nevertheless, I do not see the Jmol applet corruption problem with this older version of Java in Chrome or MSIE. Does anyone else see this problem with the new version of Firefox on Windows? It's late in Florida, so I'm not going to update Java now. I'm hoping that I get some feedback on this issue and the latest version of Java before I take that step tomorrow. Otis FIRST CONSOLE REPORT Java Plug-in 1.6.0_21 Using JRE version 1.6.0_21-b06 Java HotSpot(TM) Client VM User home directory = C:\Users\OSR c: clear console window f: finalize objects on finalization queue g: garbage collect h: display this help message l: dump classloader list m: print memory usage o: trigger logging q: hide console r: reload policy configuration s: dump system and deployment properties t: dump thread list v: dump thread stack x: clear classloader cache 0-5: set trace level to urlImage=jar:http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSign ed0.jar!/jmol75x29x8.gif Jmol applet jmolApplet0__10146987661545__ initializing AppletRegistry.checkIn(jmolApplet0__10146987661545__) 1738 script command tokens applet context: -applet-signed-threaded appletDocumentBase=http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flo t-energy.htm?model=data/cyclohexaneFlip.jmol appletCodeBase=http://chemapps.stolaf.edu/jmol/docs/examples-12/ (C) 2009 Jmol Development Jmol Version: 12.1.38_dev 2011-02-16 08:29 java.vendor: Sun Microsystems Inc. java.version: 1.6.0_21 os.name: Windows 7 memory: 5.2/16.1 processors available: 2 useCommandThread: true appletId:jmolApplet0__10146987661545__ (signed) defaults = "Jmol" backgroundColor = "lightblue" language=en_US antialiasDisplay = true loadstructcallback = "plotEnergies" animframecallback = "doHighlight" FileManager.getAtomSetCollectionFromFile(data/cyclohexaneFlip.jmol) FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol openFile(data/cyclohexaneFlip.jmol): 453 ms FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol FileManager.getAtomSetCollectionFromFile(http://chemapps.stolaf.edu/jmol/doc s/examples-12/data/cyclohexaneFlip.jmol|chxinv.xyz) FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol The Resolver thinks Xyz openFile(http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFl ip.jmol|chxinv.xyz): 413 ms reading 630 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 35 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 630 atoms created Time to autoBond: 50 ms ModelSet: autobonding; use autobond=false to not generate bonds automatically 35 models ColorManager: color "roygb" range 0.0 0.0 Model = 2, Energy = -160.4 kJ/mol Model = 3, Energy = -157.8 kJ/mol Model = 4, Energy = -154.1 kJ/mol Model = 5, Energy = -149.8 kJ/mol Model = 6, Energy = -145.3 kJ/mol Model = 7, Energy = -141.0 kJ/mol Model = 8, Energy = -137.5 kJ/mol Model = 9, Energy = -135.2 kJ/mol Model = 10, Energy = -134.2 kJ/mol Model = 11, Energy = -134.6 kJ/mol Model = 12, Energy = -136.2 kJ/mol Model = 13, Energy = -138.5 kJ/mol Model = 14, Energy = -141.1 kJ/mol Model = 15, Energy = -143.8 kJ/mol Model = 16, Energy = -146.1 kJ/mol Model = 17, Energy = -147.7 kJ/mol Model = 18, Energy = -148.3 kJ/mol Model = 19, Energy = -147.1 kJ/mol Model = 20, Energy = -145.0 kJ/mol Model = 21, Energy = -142.3 kJ/mol Model = 22, Energy = -139.4 kJ/mol Model = 23, Energy = -136.8 kJ/mol Model = 24, Energy = -135.0 kJ/mol Model = 25, Energy = -134.2 kJ/mol Model = 26, Energy = -134.7 kJ/mol Model = 27, Energy = -136.6 kJ/mol Model = 28, Energy = -139.5 kJ/mol Model = 29, Energy = -143.3 kJ/mol Model = 30, Energy = -147.5 kJ/mol Model = 31, Energy = -151.7 kJ/mol Model = 32, Energy = -155.7 kJ/mol Model = 33, Energy = -158.7 kJ/mol Model = 34, Energy = -161.0 kJ/mol Model = 34, Energy = -161.0
[Jmol-users] Calculate structure results
Hi All, I have recently discovered what I think is erroneous output for turns when using calculate structure. Beta turns contain four residues, but the segments that are colored blue after using calculate structure are from two to five residues long. Some of the ones that are three and five residues contain a hydrogen bond between the residues expected for a beta turn. It appears that some turns are being marked short by one residue and others are long by a residue. I get these results using the application with 12.0.34 and on Proteopedia by adding '?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar' to the page url. It occurs with myohemerythrin (2mhr.pdb) and domain 2 of chain a of glycogen phosphorylase. Karl Karl M. Oberholser, Ph.D.Phone: Emeritus Professor of Chemistry Voice: 717-766-0512 Chemistry & Biochemistry Dept.Fax: 717-691-6046 Messiah College e-mail: oberh...@messiah.edu P.O. Box 3049 One College Avenue Grantham, Pa 17027 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Newbie question: showing a docked receptor-ligand model (applet)
The difficulty is defining the atoms involved in the receptor...showing bonds and ribbons in the entire protein is quite easy: select protein; cartoon on; The ligand will display initially as bonds and atoms. I suspect this isn't what you want :-) Here's script for displaying bonds and atoms only within, say, 6 Angstroms of the ligand(s): select protein; cartoon only; select within(6.0,ligand);wireframe 60; spacefill 100; and if you're interested only in displaying sidechains: select protein; cartoon only; select within(6.0,ligand) and sidechain;wireframe 60; spacefill 100; You can save that script to a .spt file for easy retrieval elsewhere (and easy updating, if your fancy changes later), or you can just copy and paste it in the second argument of jmolApplet, just after "load 1.1_1.1_1__receptor.pdb." Cheers, Mike On Wed, Mar 2, 2011 at 10:17 AM, wrote: > Hello, i would like to find examples about how to define default values > for a receptor-ligand model (pdb format). > > >jmolApplet(400, "load 1.1_1.1_1__receptor.pdb"); > > > For us is useful to load the applet showing "ribbons" and "bonds" for the > receptor and "bonds" only for the ligand. > > Are any available Jmol example settings with receptor-ligand models? > Thank you. > > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Mike Evans Organic Chemistry Graduate Student Moore Group University of Illinois, Urbana-Champaign -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] how to start writing scripts
Dear Angel Herráez, Thank you so much for your quick reply. Sam 2011/3/2 Angel Herráez > Hello Sam > > Welcome to Jmol > > I'd advise that you browse the website and then the Jmol Wiki. > There is the Jmol Scripting Documentation, but that's better suited > for a more special use, when you have doubts about how to use a > command. First, you need to know that such a command exists. > > The wiki has links to pages that use Jmol and, specially, to > tutorials on its use and a book (that I wrote). Those are the best > way to start learning. > > Good luck. > When you have specific doubts, the jmol-users list is here to give a > hand. > > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] how to start writing scripts
Dear Adam Cooper, Thank you so much for your quick reply. Sam On Wed, Mar 2, 2011 at 5:18 PM, Adam Cooper wrote: > Hi - > > The best thing is to look for examples and start to adapt them to do new > things. Take it slowly; do not be too ambitious. > > Look at the jmol.js library; and note you will be using JavaScript > combined with Jmol scripting rather than Java. > > There are lots of examples and tutorials on the web: Google "jmol > tutorial"! > > Cheers, Adam > > > On Tue, 2011-03-01 at 21:44 +0530, Sam Paul D. wrote: > > Hi, > > > > I am a research scholar and I would like to start writing scripts for > > a molecule viewer using Java. Kindly suggest me how to start > > scripting and what are the basics which I have to learn. > > > > > > dsp > > > -- > > Free Software Download: Index, Search & Analyze Logs and other IT data in > > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > > generated by your applications, servers and devices whether physical, > virtual > > or in the cloud. Deliver compliance at lower cost and gain new business > > insights. http://p.sf.net/sfu/splunk-dev2dev > > ___ Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] how to start writing scripts
Looks like you've learned the first lesson already Sam -- this list is a terrific resource for even the simplest questions. Best idea I know of is to start with examples. Check out the Jmol Wiki http://wiki.jmol.org/index.php/Main_Page and documentation http://chemapps.stolaf.edu/jmol/docs and various pages in http://chemapps.stolaf.edu/examples-11 and http://chemapps.stolaf.edu/examples-12. There are some simple pages there as well as some more sophisticated ones. And remember, if there's something Jmol doesn't do that you wish it did, feel free ask. Bob Hanson On Tue, Mar 1, 2011 at 10:14 AM, Sam Paul D. wrote: > Hi, > I am a research scholar and I would like to start writing scripts for a > molecule viewer using Java. Kindly suggest me how to start scripting and > what are the basics which I have to learn. > > dsp > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
Hi Bob, Yea i think you're right, kinda pointless generating a .jvxl file. I wanted to create the jvxl file because i don't know how to enter that algorithm without opening the console window. I wrote a little Java class and i wanted it to open the .mol file along with the surface. -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Newbie question: showing a docked receptor-ligand model (applet)
Hello, i would like to find examples about how to define default values for a receptor-ligand model (pdb format). jmolApplet(400, "load 1.1_1.1_1__receptor.pdb"); For us is useful to load the applet showing "ribbons" and "bonds" for the receptor and "bonds" only for the ligand. Are any available Jmol example settings with receptor-ligand models? Thank you. -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] how to start writing scripts
Hi - The best thing is to look for examples and start to adapt them to do new things. Take it slowly; do not be too ambitious. Look at the jmol.js library; and note you will be using JavaScript combined with Jmol scripting rather than Java. There are lots of examples and tutorials on the web: Google "jmol tutorial"! Cheers, Adam On Tue, 2011-03-01 at 21:44 +0530, Sam Paul D. wrote: > Hi, > > I am a research scholar and I would like to start writing scripts for > a molecule viewer using Java. Kindly suggest me how to start > scripting and what are the basics which I have to learn. > > > dsp > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT data > generated by your applications, servers and devices whether physical, virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] how to start writing scripts
Hello Sam Welcome to Jmol I'd advise that you browse the website and then the Jmol Wiki. There is the Jmol Scripting Documentation, but that's better suited for a more special use, when you have doubts about how to use a command. First, you need to know that such a command exists. The wiki has links to pages that use Jmol and, specially, to tutorials on its use and a book (that I wrote). Those are the best way to start learning. Good luck. When you have specific doubts, the jmol-users list is here to give a hand. -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
