> > > Miguel wrote: > >>>Miguel, is this the sort of thing you are talking about >>>wanting to be able to do in Jmol? >>> >>> From something like this: >>> >>> 4.910 4.910 5.402 >>> 90.000 90.000 120.000 >>> SPGR =154 P 32 2 1 OPT = 1 >>> 1 Si1 0.48078 0.48078 0.00000 >>> 2 O2 0.15018 0.41459 0.11650 >>> >>>going to something like the first model at >>> >>>http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm >> >> >> Be advised that we got an 'ArrayIndexOutOfBoundsException' in Normix3D >> the >> first time that I followed this link > > Thanks. What happened the second time?
Worked OK >> You asked if this is the kind of thing that I want to be able to do ... >> >> I think so ... but this seems to be a much fancier version of what I was >> thinking. >> >> I was thinking something more like ... start with 1 NaCl and grow a >> 4x4x4 >> crystal. >> >> But I assume that the ideas are the same. > > right, well, the point is that usually you don't have cartesian > coordinates, so we would have to install all the symmetry knowledge > contained in that space group designation. OK. I have a very limited knowledge of fractional coordinates and space group symmetry. >>>From an implementation perspective, my thought was that you started with >>> a >> model, you applied the 'crystal 3 3 3 <otherParameters>' command ... and >> you created a new model. > > right -- something like that. It's what's behind that simple command > that's the real trick: > > -molecular vs unit cell depiction (whether you combine pieces from one > end of the unit cell with those from the other so as to complete molecules Understood > -turning space-group designations into symmetry elements I think that means 'transformations' > -applying the symmetry elements (which are often redundant) to > generate derived atom positions. OK > -building in the necessary space-group information. On this we might > be in luck: http://cci.lbl.gov/sginfo/ > > SgInfo is library of ANSI C routines > > * for the generation of symmetry matrices > > [that's us] Good > * easy on-line access to a total of 530 settings of all space > groups listed in the International Tables Volume I (1952) (ITVI) and > Volume A (1983) (ITVA) > > [ooooh, that's useful] > > and... jackpot! > > http://cctbx.sourceforge.net/ > > Here's the kind of function I like to see already present in open > source (if not Java) from > http://cci.lbl.gov/publications/download/iucrcompcomm_jan2003.pdf That is great! If it is open source then we can use the source as a reference and reimplement in Java as a 'derived work' without violating IP rights. > quartz_structure = xray.structure( > special_position_settings=crystal.special_position_settings( > crystal_symmetry=crystal.symmetry( > unit_cell=(5.01,5.01,5.47,90,90,120), > space_group_symbol="P6222" > ) > ), > scatterers=flex.xray_scatterer([ > xray.scatterer( > label="Si", > site=(1/2.,1/2.,1/3.), > u=0.2), > xray.scatterer( > label="O", > site=(0.197,-0.197,0.83333), > u=0)]) > ) > > yeah, that's it! Excellent. Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
