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* <[email protected] <mailto:[email protected]>> > Date: Sat, Feb 13, 2010 at 3:04 AM > Subject: Re: [Jmol-users] auto-orientation? > To: [email protected] > <mailto:[email protected]> > > > 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] <mailto:[email protected]> > 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
