OK, maybe an axial ratio test switch in Jmol would be useful, but as
standard I would prefer to see the assigned atom colours used for the
ellipsoids. After all, you can actually see elongated ellipsoids even
without colouring them differently. And elongated ellipsoids are the most
interesting since they may point to something special like rotational
disorder, an incipient transition etc. They should not be automatically
flagged as an error or suspect. I guess structural papers might sometimes
still be worth publishing even if the thermal ellipsoids are a bit
strange, or (heaven forbid) non-positive definite ;-) But yes, show them
as average spheres if they are non-PD.
Alan.
Brian McMahon said:
> Bob
>
> Just to keep up the flow of ideas on this, the IUCr checkCIF
> issues "ALERTS" of various levels of severity in diagnosing
> unrealistic ellipsoids according to the recipe below:
>
> PLAT_211 Test for NPD ADP's in main residue(s)
> This test reports on non-positive definite (i.e. complex and
> unrealistic)
> anisotropic displacement parameters in the main residue.
>
> Failure of this test results in an ALERT Level A.
>
> PLAT_212 Test for NPD ADP's in small moieties (solvent/anions)
> This test reports on non-positive definite (i.e. complex and
> unrealistic)
> anisotropic displacement parameters in small moieties (solvent/anion).
>
> Failure of this test results in an ALERT Level B.
>
> PLAT_213 ADP maximum/minimum ratio test for main residue
> The maximum and minimum main axis ADP ratio (Angstrom Units) is tested
> for the main residue. Large values may indicate unresolved disorder.
>
> IF ratio > 5.0 THEN issue ALERT Level A.
> IF ratio > 4.0 THEN issue ALERT Level B.
> IF ratio > 3.0 THEN issue ALERT Level C.
>
> PLAT_214 ADP maximum/minimum ratio test for small moiety
> The maximum and minimum main axis ADP ratio (Angstrom Units) is tested
> for the minor residue(s). Large values may indicate unresolved
> disorder.
>
> IF ratio > 6.0 THEN issue ALERT Level A.
> IF ratio > 5.0 THEN issue ALERT Level B.
> IF ratio > 4.0 THEN issue ALERT Level C.
>
>
> I doubt that it's Jmol's job to distinguish between "main residue" and
> "small moiety", so I would suggest allowing an optional colour scheme
> that maps ellipsoid colour to maximum/minimum main axis ADP ratio
> that runs something like this:
>
> max/min ratio > 6.0 colour ellipsoid RED
> max/min ratio > 5.0 colour ellipsoid ORANGE
> max/min ratio > 4.0 colour ellipsoid GREEN
> max/min ratio > 3.0 colour ellipsoid BLUE
> max/min ratio > 2.0 colour ellipsoid INDIGO
> max/min ratio > 1.0 colour ellipsoid VIOLET
> max/min ratio > 0.0 colour ellipsoid GREY
>
> and if non-positive definite, colour ellipsoid YELLOW.
>
> Cheers
> Brian
> _________________________________________________________________________
> Brian McMahon tel: +44 1244 342878
> Research and Development Officer fax: +44 1244 314888
> International Union of Crystallography e-mail: [EMAIL PROTECTED]
> 5 Abbey Square, Chester CH1 2HU, England
______________________________________________
Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
<[EMAIL PROTECTED]> +33.476.98.41.68
http://www.NeutronOptics.com/hewat
______________________________________________
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