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
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