I don't think that Jmol renders Hexagonal cells correctly when using fractional coordinates (at least with CML), although they look correct when using Cartesians coordinates. Looking at the entirely hypothetical HCP structure (in CML format below), I don't get what I expect to see. The Arsenic at (2/3, 1/3 ,1/2) looks to be in the wrong place, basically it should be "in the middle of the triangle made by the axes", well, you can see the HCP structure in any inorganic chemistry text book, and hopefully you can see the differences in the two files below. However we've only looked at this using Jmol-8 & CML so apologies if this has already been fixed.
using Fractional coordinates:
<molecule>
<crystal>
<scalar dictRef="cml:a">4.00</scalar>
<scalar dictRef="cml:b">4.00</scalar>
<scalar dictRef="cml:c">6.00</scalar>
<scalar dictRef="cml:alpah">90.00000</scalar>
<scalar dictRef="cml:beta">90.00000</scalar>
<scalar dictRef="cml:gamma" >120.00000</scalar>
</crystal>
<atomArray>
<atom elementType="As" xFract="0.00000" yFract="0.00000" zFract="0.00000"/>
<atom elementType="As" xFract="0.66666" yFract="0.33333" zFract="0.50000"/>
</atomArray>
</molecule>
and the same thing in Cartesian format:
<molecule> <crystal> <scalar dictRef="cml:a">4.00</scalar> <scalar dictRef="cml:b">4.00</scalar> <scalar dictRef="cml:c">6.00</scalar> <scalar dictRef="cml:alpah">90.00000</scalar> <scalar dictRef="cml:beta">90.00000</scalar> <scalar dictRef="cml:gamma" >120.00000</scalar> </crystal> <atomArray> <atom elementType="As" x3="0.00000" y3="0.000000" z3="0.000000"/> <atom elementType="As" x3="2.00000" y3="1.154701" z3="3.000000"/> </atomArray> </molecule>
regards Jon
PS - IO popularity test => CML please
-- Jon Wakelin Department of Earth Sciences University of Cambridge Downing Street CAMBRIDGE CB2 3EQ
Phone: 01223 333409
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