Thomas Stout schrieb: > Hi All -- > > Before I embark on re-inventing yet another wheel, I thought I would > ask: has anyone already created a script for choosing an optimal > orientation in which to display a given molecule? I am thinking in > terms of minimizing the overlap of atoms along the vector of view (z > axis), i.e., the best fit of atom coordinates to the xy plane... > It is quite difficult to define an optimal orientation. Even if you do it manually you have to make compromises and it depends on what you want to show. Since many PDB structures are oriented initially rather bad for viewing, we tried to find a way of optimizing the view for our automatically generated images for all PDB structures in the JenaLib (http://www.fli-leibniz.de/IMAGE.html). I first tried to use distance measurements to determine a better orientation. But this was much too slow within Jmol. So finally we ended up using the boundbox plane sizes. The method is very fast and often results in a better or equally good orientation. I currently don't have time to explain it in more detail but you can take a look at it in our Jena3D viewer, e.g.: http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh The structure is first rotated 180 degrees and then reoriented automatically. You can compare it to the initial orientation by entering "reset" into the command input field. You can take a look at the mechanism by looking at the scripts behind the standard view buttons.
Regards, Rolf ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
