>From the documentation:
*[radius option] Addition of the keyword "radius" followed by a distance in
angstroms allows definition of the radius of a modified or newly created
bond. If the modify/create option is absent, then "modify" is assumed; if
the bond type is absent, then bonds of any type are set, but their bond type
is not changed.
*Key there is that MODIFY is assumed. So you need:
connect (atomno=70) (atomno=111) hbond orange radius 0.05 CREATE
instead.
Bob
On Sun, Sep 21, 2008 at 6:56 AM, Volker Blum <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> using the latest prerelease version of jmol, prerelease 11.6.RC15, I
> have
> questions on two issues that I've found difficult for a while:
>
> 1) (minor) For two initially unconnected atoms,
>
> connect (atomno=70) (atomno=111) hbond orange radius 0.05
>
> does not work.
>
> Doing first
>
> connect (atomno=70) (atomno=111) hbond
>
> and then
>
> connect (atomno=70) (atomno=111) hbond orange radius 0.05
>
> produces the desired result. Any reason why the original command does not
> work
> out of the box?
>
>
> 2) Regarding cartoons (ribbons etc) - I have found it excessively tedious
> to
> get a ribbon into what is obviously a helix in a structure of mine. Doing
> this based on an xyz file is obviously impossible. Converting first to a
> .pdb
> file, then hand-editing the pdb file to get CA's and CB's right gets the
> ribbon for me correctly in one structure, but not in another (exactly same
> procedure).
>
> Questions:
>
> What exact information does jmol even require to safely produce a ribbon?
> For
> me, this was a rather frustrating "guessing in the dark experience.
> Empirically, it's
>
> - a pdb file
> - numbered residues, perhaps their names
> - correctly specified CA's and CB's
> - ??? what else?
>
> Is there any reason why a ribbon should not be producable by "simply"
> specifying the atoms to be connected from within jmol itself? Having such a
> feature available would be a great help ....
>
>
> thanks & best wishes
> V. Blum
>
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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
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