[Sorry, I am still not getting Jmol-users messages. So I'm slow on the
take here. I'll look through some recent archives for messages I might
have something to say about]
Alan, the latest incarnation of Jmol, 11.1.17, includes just the sort of
thing you want, although not sorted. (Come now, you can do that on your
own, right? :) )
I will use 11.1.17 syntax since this wouldn't work on earlier versions
anyway. Basically what you do is:
1) choose bondmodeOR = true or bondmodeOR = false and create a "bond
set" for the atoms you are interested in. Then format the label for the
set anyway you want.
bondmodeOR = true
theBonds = {_Si}.bonds.label("%2a1%-3i1 %2a2%-3i2 %6.3LENGTH")
The code in there is format code
%2a1 atom 1 identifier, 2 characters, right-justified
%-3i2 atom 2 index, 3 characters, left-justified
%6.3LENGTH bond length set in 6 characters, right-justified, rounded
to 3 decimal places
(another bond option is %ORDER)
now if you say
message @theBonds
you get your information:
O11 Si10 1.605
O9 Si5 1.614
O8 Si7 1.605
Si7 O2 1.614
Si7 O9 1.605
O6 Si5 1.605
O4 Si7 1.614
Si3 O11 1.614
Si3 O4 1.605
O2 Si1 1.605
Even easier, using the new Jmol.js jmolEvaluate() funcation (only at St.
Olaf, I think? -- not sure if this got into the package), on your web
page use:
var mybonds = new Array()
mybonds = jmolEvaluate('{_Si}.bonds.label("%2a1%-3i1 %2a2%-3i2
%6.3LENGTH').split("\n")
Then you have them in a nice JavaScript array you can sort anyway you
want to.
Bob
Alan Hewat
Sun, 25 Feb 2007 09:31:19 -0800
Jmol already calculates bond-lengths to decide which atoms are bonded
according to distance criteria. It would be very nice to be able to output
a list of these bond-lengths, sorted according to central bonded sites.
For example, the output obtained from
http://icsd.ill.fr/icsd/index.php?action=Bonds&id[]=72989
<http://icsd.ill.fr/icsd/index.php?action=Bonds&id%5B%5D=72989>
Then of course it would be an extra bonus to be able to output a list of
the bond angles as well, as can be done from the above URL.
Finally :-) if you have a list of bond lengths, it would be very useful
for inorganic/ionic structures to be able to calculate the bond-valence
sum around the different cations. This is simply the sum of the individual
bond valences = exp((Ro-R)/B) where R is the bond length and Ro and B are
parameters for given cation-anion oxidation states obtained from a look-up
table such as http://icsd.ill.fr/icsd/help/valence.html
The valence states would be extracted from the CIF file, as used for
drawing ionic radii. (Actually in my calculation I have a self-consistency
loop, which assumes intial valence states, calculates the valence sum for
comparison, and then if it is significantly different, uses this new value
as the supposed valence state to select new Ro and B parameters).
The bond valence sum is a very important check on the correctness of a
structure. If it unreasonable then almost certainly something is wrong
(atom coordinates, disorder, stoichiometry etc...)
Alan.
_____________________________________________________________
Dr Alan Hewat, ILL Grenoble, FRANCE <[EMAIL PROTECTED]>fax+33.476.20.76.48
+33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/
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[Jmol-users] Bond lengths & valence sum calculation with Jmol?
Alan Hewat
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