Hey Angel
You can see the structure here:
http://www.eden.rutgers.edu/~tz69/Catalyst/Catalyst.htm
Just right click the structure, file, save the copy, you can get the file.
you can see many tbu-groups don't bond to P
I wonder if i can change the default value for judging bond forming set in
Jmol.
I mean i don't need to add set bondTolerance each time when i add a
structure into the page
In my case like the C-P bond's threshold. Because i have many such
files...Changing them manually will be time cost.
Thank you so much
Tian
2012/7/16 Angel Herráez <[email protected]>
> Hello Tian
>
> Jmol draws bonds if the distance between the atoms falls within some range
> of the sum of van der Waals radii for those two elements.
> Or when the file includes bond information.
> Or when there is an explicit connect command in JmolScript
>
>
> > When I open my structure I can always see some bonds break, though they
> are supposed to be
> > bond.
>
> Supposed by what rule?
> Can you share your file for us to look at?
>
>
> > I think there are some parameters to define the threshold in J mol, but
> I don't know where are
> > they, and how to change them......
>
> Yes, I think there is one that controls the threshold. Otherwise, you can
> specify, create and delete bonds at will using the "connect" command.
>
> ...
>
> Ah, there you are:
> set bondTolerance
> http://chemapps.stolaf.edu/jmol/docs/#setbondstyles
>
>
>
>
>
>
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