(Arghh... stupid web mail. I already types a lengthy reply when my webmail reloaded the send page :( OK, one more time... )
> So, Egon, where did that capability go? It was removed? Miguel basically rewrote most of the Jmol code, while I continued in the b6 branch to release Jmol 6 up to Jmol 9. Jmol 6-9 worked with CDK as data source, but it turned out to be not efficient memory wise for good rendering speeds. Therefore, Miguel rewrote the data classes, and put a JmolAdapter in front of it, to allow flexibility with the data classes used. This allows for example, Jmol still to be used with the CDK classes, while the renderer sort of caches the data internally in a fast data structure. This feature did not really got removed, but not ported from the b6 back to HEAD either. > Please take a look now at > > http://www.stolaf.edu/people/hansonr/jmol/test/proto/sym.htm > > and tell me what you think. -- just my prototype here. Looks good! > load quartz.cif;set showUnitCell on > # standard load reads only the file data -- no symmetry applied > load "quartz.cif" {2 2 2};set showUnitCell on > # note that quotation marks REQUIRED when the number of unit cells > is given This cannot be split up this in steps: 1. apply symmetry operations 2. apply lattice growing So, something like: load quartz.cif; set showUnitCell on set spacegroup p1 # to apply the symmetry operations set spacegroup original set lattice {2 2 2} because the growing has to be done on loading, right? > load calcite.cif;set showUnitCell on > load "calcite.cif" {3 2 1};set showUnitCell on > load maleic.cif;set showUnitCell on > load "maleic.cif" {1,1,1};set showUnitCell on What is the meaning of the ',' in the lattice specification? BTW, Jmol 9 supported a range, instead of an integer. For example, 0,0,0 was the unit cell, so negative numbers would grow in one direction while positive numbers would grow in the other direction. So, {-1,1; -1,1; -1,1} would create a 3x3x3 lattice, with the original unit cell in the center. > # note that this file has 18 models, each with a different unit cell OK, is sort of what I expected but not quite. I would suggest to either: 1. show only the atoms of this unit cell in connected manner, or 2. show only the atoms that physically are in the unit cell box, which would break connectivity. Now it does a bit of both, which is confusing. > set perspectiveDepth off > select symmetry;color green # select only those atoms generated by > symmetry operations > select not symmetry;color yellow # select only the original atoms > prior to symmetry operations Very nice. > frame 1 > frame next > frame prev > # an optional integer parameter right after the file name indicates > WHICH model to load > load "maleic.cif" 3 {2,2,2};set showUnitCell on > load "maleic.cif" 6 {1,1,1};set showUnitCell on I like the selection of the frame number. Is that new too? > set showUnitCell off > set perspectiveDepth on Egon ------------------------------------------------------- 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-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
