Warren Gallagher wrote: > 3. October, 2006 > > Bob, > > I have been experiencing Jmol hanging up and becoming unresponsive > when the size of the problem I ask it to perform becomes large. Two > examples: > > 1. When looking at the relatively small protein, flavodoxin (1flv), I > am able to use the "isosurface" command to draw a solvent surface > around the flavinmononucleotide ligand (31 atoms), ["isosurface select > (ligand] ignore(not ligand) solvent"], but when I attempt to use the > same command on the protein portion of the molecule (1326 atoms) > ["isosurface select(protein) ignore(not protein) solvent"], Jmol > becomes unresponsive and no surface is generated.
new algorithm: 18 seconds on my machine for isosurface delete select(protein) ignore(not protein) solvent 6 seconds for isosurface delete select(protein) ignore(not protein) sasurface 0.0 By the way, I added "molecular" as the equivalent of "solvent" (it's the same surface, right? -- where solvent meets molecule). So this works in 10.9.71: isosurface delete select(protein) ignore(not protein) molecular > > 2. When looking at the structure for the 50S subunit of the 70S > ribosome (2j01), which was reported in this week's issue of Science, > I am able to load the structure into Jmol (89408 atoms), but when I > attempt to render the structure with the "cartoon on" command, Jmol > hangs up and becomes unresponsive; no cartoons are generated. I am > not having this problem with version 10.3.1. The Jmol Java console > window gives the following message: > thanks -- misplaced code line. now fixed. What an incredible structure! Bob ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
