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> 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
> > 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
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> 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
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Jmol-users mailing
> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
