[Jmol-users] crystal structures and symmetry

[Bob H. <ha...@st...>]

Jmol users,

I am experimenting with adding the capability for Jmol to read the 
symmetry operations in selected file readers. These look like this:

x,y,z
-x,1/2+y,1/2-z
-x,-y,-z
x,0.5-y,0.5+z

I have a working prototype for CIF files that can be played with at

http://www.stolaf.edu/people/hansonr/jmol/test/proto/sym.htm

Questions I have:

1) Who is interested in such capability?

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?

3) Notice that the maleic.cif file has 17 completely different 
structures, one per frame. That look OK?

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?

5) Is it important to be able to select specific molecules (i.e. 
covalently bonded sets of atoms)?

6) Is it important to be able to select just the file's "primitive" data 
set -- that is, without symmetry operations applied?

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"?

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?

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?

Thanks in advance,

Bob Hanson