I've gone through the entire list at http://wiki.jmol.org/index.php/Merge_10.9_-_10.3 and in each case carefully looked at the diffs and have either made the change, discarded it as irrelevant, or marked it as "LATER", meaning maybe sometime later; not critical. Nico has done a lot of this as well.
And, yes, there were some substantial things I missed -- some nice changes to Polyhedra scripting that I only did in 10.3 and then forgot about; some clean up of the autobonding. In the process, I took the opportunity to clean those up a bit more, and because it caused me so much grief, I've moved some default values from ModelManager to StyleManager and added a Logger.info() flag whenever settings are changed. I'm wondering why 10.9 but NOT 10.3 had a major addition to the application bond preferences dialog. I've left those in, figuring that more control is better, but I'm a bit curious as to why the difference. All the important readers now support crystallographic extensions -- adding spacegroup and unitcell specifications to the load line. This is really quite fun. I ran into some interesting issues with protein PDB crystal structures, and now I feel I've definitely got those bugs worked out. Still, some more exercise with protein crystal structures would be nice. Note that in the case of PDB and mmCIF files we are reading the Cartesian-to-Fractional coordinate data directly. I note that this matrix APPEARS to have an error in 1CRN (specifically). I've studied this now all day, and I can't see any other possibility. It's the sign of one of the terms. Since it appears to only be 1CRN and not other CIF/PDB files I've looked at, I think it must be a CIF/PDB error. I've sent a note to RCSB. So as soon as people are satisfied that the CML and RES readers are doing what they are supposed to do, I think we are ready. The documentation is up to date; I've been updating it as I've modified. Bob ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
