Not sure if its helpful, but this page shows a translucent isosurface for water colored by molecular electrostatic potential, in Jmol 12.3.22. -Eric
http://proteopedia.org/wiki/index.php/User:Eric_Martz/Sandbox_8 At 6/23/12, Daniel Aioanei wrote: >I'm not able to compute the sasurface of a water (H2O) molecule: > >$ isosurface test sasurface 1.4 >test created with cutoff=0.0; isosurface count: 0 >$ show isosurface >$ > >After the above commands, I cannot see any surface drawn, and in fact >after issuing the "show isosurface" command, it's not possible any >more to rotate the molecule in the GUI. With other (larger) molecules >the above procedure works as expected. > >Interestingly, if I create a "molecular" surface instead, still no >surface is drawn, the molecule can still be rotated and the console >output looks like this: > >$ isosurface test molecular >test created with cutoff=0.0; isosurface count: 1 >$ show isosurface ><?xml version="1.0"?> ><jvxl version="2.2" jmolVersion="Jmol 12.3.32_dev 2012-06-20 18:17" >xmlns="http://jmol.org/jvxl_schema"; >xmlns:cml="http://www.xml-cml.org/schema";> >... ></jvxlEdgeData> ><jvxlInvalidatedVertexData bsEncoding="base90+35" count="736" >len="736"> -#}3+ </jvxlInvalidatedVertexData> ></jvxlSurfaceData> ></jvxlSurface> ></jvxlSurfaceSet> ></jvxl> > >I encountered the above behaviour on a very recent jmol codebase >checked out from svn (jmol revision 17324) with Java 7u[4-5] on Mac OS >X and Fedora Linux. > >------------------------------------------------------------------------------ >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 ------------------------------------------------------------------------------ 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
