Many thanks !
With the revised version I managed to make the figure. It was a bit laborious
because one have to define every tetrahedron (actually a pair is also
allowed). One more thing is that atom picking is broken in the modified Jmol
version. Though I hope this feature will move to the main branch.
The ASSIGN command is also quite useful. Several times I made exactly the same
thing, but in much less elegant way.
Nikolay
On 09/07/12 20:00, Robert Hanson wrote:
> OK, here's how it works. This is probably not documented, but it is the
> way the state works, so it is fine to use it.
>
> All polyhedra need a reference atom, but that atom can be any atom,
> including one of the face atoms. It doesn't have to be a "central" atom.
> The key is the (undocumented) TO option:
>
> polyhedra ({2}) TO ({2 3 4 5})
>
> The ({...}) notation is an atom "bitset" -- it's a list atom INDEXES
> (not atom numbers).
>
> But realizing now that that's not really necessary, and that maybe this
> would be useful outside the context of a state, I have this for you:
>
> http://chemapps.stolaf.edu/jmol/Jmol-13.zip
>
> With this minor revision, now you can use any atom expression:
>
> polyhedra {H7} to {H3 or H5 or H6 Or H7}
>
> No center here, just faces among the set H3, H5, H6, and H7. The color
> and display characteristics will depend on H7.
>
> Bob
>
>
>
> On Fri, Sep 7, 2012 at 12:24 PM, Pshemak Maslak <p...@chem.psu.edu
> <mailto:p...@chem.psu.edu>> wrote:
>
> On 9/7/2012 1:03 PM, Robert Hanson wrote:
>> The polyhedron needs a central atom. But you can add that
>> yourself. The command appears to be undocumented --
>>
>> assign {attachmentAtom} "Symbol" {x y z}
>>
>> For example:
>>
>> assign atom {atomno=14} "Cl" {2 3 4}
>>
>> That position {2 3 4} could also be an average position of a
>> number of atoms:
>>
>> assign atom {atomno=14} "Cl" {2 3 4} {atomno=14 or atomno=13 or
>> atomno=12 or atomno=11}
>>
>> then you would also need to do the connections before creating the
>> polyhedra.
>>
>> HOWEVER, with a bit of a tweak of Jmol, I can make this possible
>> without connecting the atoms. You will still need a central atom,
>> though. Let me get back to you on this.
>>
>> Bob
>
>
> Could the tweak include the option of drawing polyhedra if not all
> "vertices" are present? Such as a tetrahedron for ammonia or water?
>
> Something that would draw a polyhedron when the central atom and a
> number of vertices is specified with the size equal the specified
> bond (something like O1 4 O1-H 1 for water)..
>
> I know I am asking too much, but if you are tweaking it...
>
> Thanks
>
> PM
>
>
>
>
>
>
>>
>>
>> On Fri, Sep 7, 2012 at 8:16 AM, Nikolay Bogdanov
>> <nikol.bogda...@gmail.com <mailto:nikol.bogda...@gmail.com>> wrote:
>>
>> I'm trying to make a figure showing the coordination of metal
>> ions in crystal - they form network of tetrahedra. I can do
>> this with bonds, but the
>> figure looks confusing. It would be much more clear with
>> opaque tetrahedrons.
>>
>> As I understand Jmol builds polyhedra around some central
>> atoms, which are missing in my case. So I wonder is there a
>> way to build the polyhedra just
>> from bonds.
>>
>> Thanks,
>> Nikolay
>>
>>
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>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> 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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>> threat landscape has changed and how IT managers can respond. Discussions
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>>
>>
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>
>
>
> ------------------------------------------------------------------------------
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> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
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>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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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> threat landscape has changed and how IT managers can respond. Discussions
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