Ah, the central cavity! This is because, if you look VERY carefully, there is a little bridge between the channel and that interior piece. I think if you tweak the parameters, you can break that bridge, and it will not be part of the pocket subset. Maybe...
Bob Christian Baerlocher wrote: >Dear Bob, > >Thanks again very much. It is really very very useful (and beautiful, >of course). > >I have now implemented it in a test version with our database. Look at > >http://topaz.ethz.ch/IZA-SC/StdAtlasj.htm > >and select a 3 letter code from the matrix (LTA you know already, but >try IMF or MOZ or whatever, they all look very nice) and click on >Live 3D drawing. > >I found one small problem with -CLO. This has a very large cage, and >it seems it generates a cavity in the center which should not be >there. Is there a way to avoid it? I am not sure I understand fully >the parameter after "cavity". > >Christian > > > > >On Apr 18, 2007, at 8:48 AM, Bob Hanson wrote: > > > >>Glad to hear it, Christian. I saw the zeolite case as a nice >>opportunity >>to try a few new things. Interesting cavities and channels and >>"pockets" >>in there. The backlit/frontlit business will be quite useful. This is >>applicable to any sort of isosurface, but especially useful for >>molecular/solvent surfaces. >> >>When Nico gets back from his travels he can update SourceForge. For >>now >>you can get JmolApplet.jar in >> >>http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11 >> >>(files should show up there within the hour; I'm doing some final >>testing) >> >>Bob >> >>Christian Baerlocher wrote: >> >> >> >>>Dear Bob, >>> >>>Wow, this is great! Thanks a lot. You solved all my problems, even >>>those I was going to ask you: backlit etc. >>> >>>When can I download the new version? >>> >>> >>>Christian >>> >>> >>> >>>On Apr 17, 2007, at 4:19 AM, Bob Hanson wrote: >>> >>> >>> >>> >>> >>>>Dear Christian, >>>> >>>>Take a look at >>>>http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/ >>>>new.htm >>>> >>>>Near the top you will see a link for lta-11(1).xyz and some new >>>>isosurface options that I think you will benefit from. >>>> >>>>Bob Hanson >>>> >>>> >>>> >>>>-------------------------------------------------------------------- >>>>-- >>>>--- >>>>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 it now. >>>>http://sourceforge.net/powerbar/db2/ >>>>_______________________________________________ >>>>Jmol-users mailing list >>>>[email protected] >>>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>>> >>>> >>>--------------------------------------------------------------------- >>>---- >>>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 it now. >>>http://sourceforge.net/powerbar/db2/ >>>_______________________________________________ >>>Jmol-users mailing list >>>[email protected] >>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> >>---------------------------------------------------------------------- >>--- >>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 it now. >>http://sourceforge.net/powerbar/db2/ >>_______________________________________________ >>Jmol-users mailing list >>[email protected] >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > >------------------------------------------------------------------------- >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 it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- 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 it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
