Hi Roberto, I had what looks like a similar problem to yours about a year or so ago with .cube files for molecular orbitals generated from Q-Chem. We posted a bug report (http://sourceforge.net/tracker/?func=detail&aid=3132575&group_id=165310&atid=835077), and it appears that they made a patch in response to the issue. I have not used Avogadro for a while but thought this may be useful to know.
Best, Eric Isaacs On Tue, Jun 5, 2012 at 12:09 PM, Roberto Di Remigio <roberto.diremi...@gmail.com> wrote: > Dear all, > I am trying to plot an electron density starting from a cube file, whose > header is reported below: > cube file > generated by DIRAC > 3 -10.000000 -10.000000 -15.701543 > 80 0.253165 0.000000 0.000000 > 80 0.000000 0.253165 0.000000 > 80 0.000000 0.000000 0.397507 > 53 53.000000 0.000000 0.000000 0.000000 > 53 53.000000 0.000000 0.000000 5.701543 > 53 53.000000 0.000000 0.000000 -5.701543 > > To generate the plot, I loaded the file then went to Extensions -> Create > Surfaces and select cube files in both dropdown menus. > > The problem I encounter is that the plotted density is shifted from the > atoms, without any particular reason apparently. I attached a png of the > Avogadro rendering and the ParaView rendering, so that you can see more > clearly what I mean. > Best regards. > > -- > Roberto Di Remigio > > > ------------------------------------------------------------------------------ > 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/ > _______________________________________________ > Avogadro-Discuss mailing list > Avogadro-Discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > ------------------------------------------------------------------------------ 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/ _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
