> 1) Who is interested in such capability? Study of packing patterns in small organic chemistry crystallography is a growing field. Figures in papers are hard to read, Jmol with structures as supporting material will be very valuable. (and such websites in general of course).
I would recommend downloading Jmol 9. It has support for growing the lattice beyond one unit cell. > 2) How do those models look so far? Do you think they look "normal" or > "natural" with the whole molecules extending a bit from the unit cell > like that? For me, as an organic chemist who worked in crystal structure classification and clustering, this is the preferred way. > 3) Notice that the maleic.cif file has 17 completely different > structures, one per frame. That look OK? Are those polymorphs? Different compounds? > 4) If we were to implement something that allowed one to "grow" a > crystal -- designate how many unit cells to combine, and in what > direction, what's the best way to do that? I mean, what sort of commands > might accomplish this, in your mind? See what Jmol 9 was capable of. > 5) Is it important to be able to select specific molecules (i.e. > covalently bonded sets of atoms)? For organic compound crystals, I would expect that something like 'select unitcell (0,0,0)' would indeed select the atoms in the molecules whose center of mass is in that unit cell; this would match those shown in the maleicacid.cif demo... > 6) Is it important to be able to select just the file's "primitive" data > set -- that is, without symmetry operations applied? That would allow to color those atoms differently then the other unit cell when rendering an extended lattice... > 7) Is it important to be able to control how the file loads -- applying > symmetry or not? If so, should the default be "no symmetry appied", or > should it be what you see here, "symmetry applied and normalized," or > should it be "symmetry applied and all atoms within the boundaries of > the unit cell"? I would prefer to not apply symmetry upon load, and have a script command for converting to P1. > 8) Am I right in my analysis that although SHELX files DO have the SYMM > line, the complications involving LATT make it VERY complicated to do > this correctly within that file type? This was no problem with the SHELX files I used in the past, but the bellow page indeed seems to indicate that LATT is used to work around certain problems... http://www.sdsc.edu/CCMS/Packages/cambridge/prequest/zprq4020.html But can't really comment on this. > 9) Are there any complication with mmCIF files? For example, these files > don't have _symmetry_equiv_pos_as_xyz listed, so perhaps none of this > applies to them? No idea. 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
