Can you define more precisely what is you are doing to position according to the boundbox? Jmol has, since ancient times, commands to orient according to Top, Bottom, etc, which I'd say are related to the boundbox. In fact, I've never seen much advantage in having them in the menus for example. Maybe there was a meaning after all!
On 16 Feb 2010 at 20:32, Rolf Huehne wrote: > Thomas, > I am gladI could help you and I don't have any objections to both proposals. > > Regards, > Rolf > > Thomas Stout schrieb: > > Rolf -- > > > > I have now had a chance to locally implement your approach to this > > question of "optimal orientation". What you have done is exactly what > > I wanted & was proposing putting together! Your boundbox approach is > > much more efficient than my original thought of minimzing coordinate > > "overlap" and is working very, very nicely. > > > > I think that this may be a generally useful "tool" -- it may not be > > perfect in all cases, but it is certainly the >95%-solution. Would you > > be willing to post the code to the PyMOL wiki? Alternatively, would you > > mind if I suggested to Bob & Angel and everyone that an "orient" > > functionality be added to Jmol? I think it's very useful & should be > > generally available..... > > > > Many thanks, > > Tom > > > > > > > > ---------- Forwarded message ---------- > > From: *Rolf Huehne* <rhue...@fli-leibniz.de <mailto:rhue...@fli-leibniz.de>> > > Date: Sat, Feb 13, 2010 at 3:04 AM > > Subject: Re: [Jmol-users] auto-orientation? > > To: jmol-users@lists.sourceforge.net > > <mailto:jmol-users@lists.sourceforge.net> > > > > > > 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 > > Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ------------------------------------------------------------------------------ > 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 > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
