On Mon, Aug 6, 2012 at 4:58 AM, elleB <livyb...@hotmail.com> wrote: > I am attempting to use Avogadro to visualize a polymer network > produced by a self-written MD code. > It is a coarse-grained model, so the atom types I have used are > abitrary. > The output consists of bead co-ordinates and connectivity, which I > wrote into a .cml file. > > I am having some problems representing bonds which cross the > periodic boundary of my cell. > Must I duplicate the cells in the .cml file to show these bonds, > or is there a way to wrap the bonds around using a unit cell?
Unit cell support in Avogadro is somewhat lacking. Currently, there is no way to get a good visualization of intercellular bonding in the public avogadro releases. I have a patch that adds the ability to render bonds across cells, but it is a bit expensive for large cells, and still a little rough around the edges, so it hasn't made it into Avogadro 1.x (And it likely never will -- most of my development efforts will go into the 2.0 release for now). I'd really like to get more of this sort of functionality into that release. This mailing list discussion from a few months ago talks about rendering these bonds: http://www.mail-archive.com/avogadro-devel@lists.sourceforge.net/msg00435.html And here's a link to the patch on github if you'd like to try it: https://github.com/dlonie/avogadro/commits/ENH_intercell_bonds > Also, is there a way to define the unit cell in a .cml file > instead of going through the GUI? Sure: <molecule> <crystal> <scalar title="a" units="units:angstrom">3.000000</scalar> <scalar title="b" units="units:angstrom">3.000000</scalar> <scalar title="c" units="units:angstrom">3.000000</scalar> <scalar title="alpha" units="units:degree">90.000000</scalar> <scalar title="beta" units="units:degree">90.000000</scalar> <scalar title="gamma" units="units:degree">90.000000</scalar> </crystal> <atomArray> [...] </atomArray> </molecule> Hope this helps, Dave ------------------------------------------------------------------------------ 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
