Hi Bob using # Jmol state version 13.0.RC2 2012-07-21 19:52;
> load =1u19; > > OK, here you have three isosurfaces. set 1 is the outer set, but there > are two cavities, each of which is big enough to hold a molecule of > water. there is something strange going on, I still get those fragments load =1u19; isosurface resolution 2.0 solvent; isosurface set 2; pngj: https://www.dropbox.com/s/o6q7dudwj48k4ht/1u19.png > By the way, you might want to use isosurface SOLVENT instead of > MOLECULAR. Do you really want the surface around the water molecules? these were just minimal examples nothing I actually used, thanks though > # trying to get the isosurface into the state to trade a slightly > bigger file size for faster loading > > > use > > write xxx.jvxl > > then immediately replace the isosurface with that using > > isosurface delete > isosurface "xxx.jvxl" > > then write the file as a PNGJ or JMOL. This should be very compact and > very fast to load. yes that's ok but I did not mention that I want to use this in the applet and make it as automatic as possible, without the detour to the file system, which requires user interaction. The problem seems to be in jmol.shapesurface.Isosurface.java::getMeshCommand() cmd = TextFormat.simpleReplace(cmd, ";#", "; #"); int pt = cmd.indexOf("; #"); if (pt >= 0) cmd = cmd.substring(0, pt); We could look for " inline " in cmd? Ahh, thats not enough, as you can do "isosurface ID inline inline @tmp". A regex perhaps: if( cmd.toLowerCase().indexOf("inline") >= 0 && !cmd.matches("(?i)id\s*['\"]?\s*inline\s*['\"]?") ){ // not tested cmd = TextFormat.simpleReplace(cmd, ";#", "; #"); int pt = cmd.indexOf("; #"); if (pt >= 0) cmd = cmd.substring(0, pt); } Well, not perfect, then we would not strip comments from the inline command. How did one get these comments anyway? Alex ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
