Re: [Jmol-users] Jmol 11.5.40, Bij and Betaij

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

Alan, can this be real?

_atom_site_aniso_label
_atom_site_aniso_type_symbol
_atom_site_aniso_B_11
_atom_site_aniso_B_22
_atom_site_aniso_B_33
_atom_site_aniso_B_12
_atom_site_aniso_B_13
_atom_site_aniso_B_23
Nb1 Nb0+ 0.33(3) 0.44(2) 0.75(3) 0.165(15) -0.03(3) -0.015(15)
Nb2 Nb0+ 0.53(2) 0.84(3) 0.51(3) 0.42(2) -0.00(1) -0.00(1)
Nb3 Nb0+ 0.07(3) 0.23(2) 0.62(3) 0.035(15) 0.14(3) 0.07(2)
Nb4 Nb0+ 0.43(2) 0.43(2) 0.52(1) 0.19(2) 0.03(2) 0.07(3)
Si1 Si0+ 0.01(8) 0.73(7) 1.00(11) 0.005(40) -0.07(9) -0.035(45)
Si2 Si0+ 0.62(9) 0.31(6) 0.61(10) 0.31(5) 0.09(8) 0.045(40)
Si3 Si0+ 0.41(6) 0.37(9) 0.85(10) 0.19(5) 0.09(5) 0.18(10)
P1 P0+ 0.47(7) 0.47(7) 0.31(13) 0.23(4) 0. 0.
P2 P0+ 0.6(2) 0.6(2) 0.3(3) 0.3(1) 0. 0.
#End of data_155350-ICSD


Check out that Si1 and Nb3 B_11 value. These are displaying in Jmol as 
very flat disks; so I think Jmol is doing it correctly. Oh, I see the 
note now:


	R=0.027800 : XDS
At least one temperature factor is implausible or meaningless but agrees 
with the value given in the paper.



Bob


Alan Hewat wrote:

>Bob, you should have access to the full ICSD database on
>http://icsd.ill.fr/icsd/index.php For example, you can search for
>3-element compounds with hexagonal symmetry and anistropic Bij with:
>http://icsd.ill.fr/icsd/index.php?action=Search&elementc=3&system=HE&remarks=AHT+Bij
>
>Select some of the results (left hand check boxes) and click the CIF
>button to export the CIFs. Or else click on the individual formulae to
>bring up the Jmol window.
>
>Alan.
>
>On Mon, Jun 9, 2008 at 5:46 PM, Bob Hanson <ha...@st...> wrote:
>  
>
>>I definitely need some of these files for testing, preferably with some
>>output image to use to verify. hexagonal lattice would be good.
>>
>>
>>Alan Hewat wrote:
>>
>>    
>>
>>>Oops! For B_i_j and Beta_i_j CIF files below read B_ij and Beta_ij. Alan.
>>>
>>>Alan Hewat said:
>>>
>>>      
>>>
>>>>I have finally sorted out ICSD to search for papers reporting Uij, Bij,
>>>>or
>>>>Betaij and to output these as CIF's. (Although Beta_i_j is not officially
>>>>defined as a CIF field, there are hundreds of older papers that use it,
>>>>and also B_i_j). For example the following will find 3-element
>>>>structures reporting Bij:
>>>>
>>>>http://icsd.ill.fr/icsd/index.php?action=Search&elementc=3&remarks=AHT+Bij
>>>>Clicking on the resulting formulae should bring up the Jmol window with
>>>>default anisotropic ellipsoids. (The CIF file can be checked as usual
>>>>from
>>>>the Jmol menu).
>>>>
>>>>The problem is that while it works for Uij with Jmol 11.5.37 when I
>>>>updated to 11.5.40 to try to get it to display Bij, the Jmol window never
>>>>finished loading. Even when I backtracked to 11.5.37 on the server, the
>>>>client still tried to use 11.5.40 until I opened the Java control panel
>>>>and cleared the Java cache. (I had also updated to the latest JRE v6
>>>>update6 which didn't help).
>>>>
>>>>So, is there a problem with 11.5.40 or is it just my XP Java
>>>>installation?
>>>>I guess Beta_i_j CIF files are not recognised even in 11.5.40, but as I
>>>>said, ICSD now finds hundreds of them :-) I would rather report the
>>>>original data than to convert them to Uij.
>>>>
>>>>Alan.
>>>>        
>>>>
>______________________________________________
>Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
><Alan.Hewat@NeutronOptics.com> +33.476.98.41.68
>      http://www.NeutronOptics.com/hewat
>______________________________________________
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900