Hi Geoff, I am attaching the file (a few frames of it). The bond dissapears because I am using the "dynamics bonds" feature.
Thank you, Xavier On Tue, Jan 14, 2014 at 9:27 PM, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: > The issue would likely be with the underlying Open Babel library. I thought > we had a special case for detecting H2, but it's possible there's a bug in > bond detection. > > Can you send me the file? > > I'm also a bit confused why the bond disappears after the first frame when > drawn by hand, but I'll investigate. > > Thanks very much, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geo...@pitt.edu > web: http://hutchison.chem.pitt.edu/ > > On Jan 13, 2014, at 11:53 AM, Xavier Andrade <xav...@tddft.org> wrote: > >> Hi, >> >> I am trying to render an animation that involves H2 molecules with >> Avogadro. The problem is that Avogadro is failing to recognize and >> draw the bond between the two hydrogen atoms in the H2 molecules, it >> just draws two isolated H atoms. The atoms are initially set at the >> experimental distance of 0.74 Angstrom. >> >> Since I need the bonds to change dynamically, drawing the bond by hand >> is not a solution, as it is lost after the first frame. >> >> Can you suggest me how to solve this problem? Is it possible to >> configure the cutoff distance for bonds or something like that? >> >> Thank you, >> >> Xavier >> >> PS: I am using Avogadro from Debian Sid: Application Version 1.0.3, >> Library Version 1.0.3, Open Babel 2.3.2 and Qt Version: 4.8.6. >> >> ------------------------------------------------------------------------------ >> CenturyLink Cloud: The Leader in Enterprise Cloud Services. >> Learn Why More Businesses Are Choosing CenturyLink Cloud For >> Critical Workloads, Development Environments & Everything In Between. >> Get a Quote or Start a Free Trial Today. >> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk >> _______________________________________________ >> Avogadro-Discuss mailing list >> Avogadro-Discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Avogadro-Discuss mailing list > Avogadro-Discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
h2.xyz
Description: Protein Databank data
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