> I saw the message about using the Jmol Application and > have been trying it for the autobond issue. I have tried > running the script "set autobond off;" > before loading one of the xyz files and get a message of: > > setting:autobond > > viewer.setBooleanProperty(autobond,false) - unrecognized
You do not have the correct/current version of the Jmol Application. (Recall that I sent the JmolApplet*.jar files to you separately via email) Download version 10.00.22 from www.jmol.org/files Version 10.00.22 includes a special feature just for you: The 2nd line of a .xyz file is a name/comment. If that line ends in the string "#noautobond" then Jmol will not bond the atoms. This is independent of the 'set autobond off' setting. Modify your program that is generating the .xyz files to add the string "#noautobond" to the 2nd line of the file and your life will get simpler. > When the file loads I then get an error message that the > "maximum auto bond count reached". Maximum auto bond count is currently set to 20. If an atom has more than 20 bonds then this message appears. > Thinking about it this kind of makes sense with the files > I have been testing. The ones that work "best" have the > "lowest" atom density and would generate the fewest number > of bonds based on interatomic distances, clearly seen when > I leave the wireframe frame command on. Correct > The most problematic files are the ones with the highest > atom density, which would generate the greatest number > of bonds. These files will load eventually but because > of the high atom density there are a hugh number of > bonds. Yep. > The file that does not work at all is an animated xyz > file (1000 atoms in 1000 frames) and for the animation > to show what I need it starts > with 999 atoms all at the origin, the worst possible case. Perhaps you missed my response on the mailing list. 1 million atoms will never work in the applet. It might work in the application, but you will need to start the application with more virtual memory for Java. > It would appear from the error message that the > set autobond off command is > not functioning the way I would expect. Test A - set autobond off 1. download 10.00.22 from www.jmol.org/files 2. start Jmol application 3. issue script command 'set autobond off' 4. load up a .xyz file (not the 1000x1000) 5. observe that it loads quickly and that there are no bonds 6. exit Jmol Test B - #noautobond 1. add '#noautobond' to the 2nd line of a .xyz file (not the 1000x1000) 2. start Jmol application 3. load noautobond.xyz 4. observe that it loads quickly and that there are no bonds 5. exit Jmol application Test C - more memory 1. start Jmol application with 1.5G memory using the command line java -Xmx1500M -jar Jmol.jar 2. 'set autobond off' 3. load 1000x1000.xyz 4. it *probably* will work 5. report back to me a. whether or not it worked b. performance numbers c. your hardware configuration Miguel ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] ----- ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
