Hi,
Thanks for the information about how to store the partial charges and
periodic information in xyz file.
After looking through the various menus, I couldn't figure out how to
display the partial charge information.
I'm using jmol version 11.8.7.
Are the partial charges supposed to show up as color variations or as
numeric labels next to the atoms?
How does one turn on the display of partial charges?
Sincere thanks,
-Tom
> jmolscript: load "" {1 2 1} spacegroup "x,y,z;x,y,1-z" unitcell {6.0 6.0 5.0
> 90 90 90}
------------------------------
>
> Message: 5
> Date: Mon, 26 Oct 2009 22:11:56 -0500
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] simplest file format to store periodic
> structures and partial atomic charges for visualization in jmol
> To: [email protected]
> Message-ID:
> <[email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Tom, you are in luck!
>
> Just add a Jmol LOAD command as the comment in the XYZ file:
>
> 12
> jmolscript: load "" {1 2 1} spacegroup "x,y,z;x,y,1-z" unitcell {6.0 6.0 5.0
> 90 90 90}
> C 1.38480 0.00000 0.00000 1.0 1.38480 0.00000 0.00000
> C -1.38480 -0.00000 0.00000 0.9 -1.38480 -0.00000 0.00000
> C 0.69240 1.19927 0.00000 0.3 0.69240 1.19927 0.00000
> C 0.69240 -1.19927 0.00000 -0.3 0.69240 -1.19927 0.00000
> C -0.69240 -1.19927 0.00000 0.3 -0.69240 -1.19927 0.00000
> C -0.69240 1.19927 0.00000 0.6 -0.69240 1.19927 0.00000
> H 1.22858 2.12797 0.00000 0.4 1.22858 2.12797 0.00000
> H 1.22858 -2.12797 0.00000 0.5 1.22858 -2.12797 0.00000
> H -1.22858 -2.12797 0.00000 0.6 -1.22858 -2.12797 0.00000
> H -1.22858 2.12797 0.00000 0.8 -1.22858 2.12797 0.00000
> H -2.45717 -0.00000 0.00000 0.0 -2.45717 -0.00000 0.00000
> H 2.45717 0.00000 0.00000 -1.3 2.45717 0.00000 0.00000
>
> That fourth column is the partial charge. The last three columns are bogus
> vibrations -- you won't need those.
>
> Here "jmolScript:" indicates an embedded command, and
>
> LOAD "" {1 2 1} spacegroup ... unitcell ...
>
> tells Jmol to reload the file with that set of load parameters.
>
> All coordinates are considered Cartesian -- don't use unit coordinates here.
>
>
> Bob
>
> On Mon, Oct 26, 2009 at 4:36 PM, Thomas Manz <[email protected]> wrote:
>
>> Hi,
>>
>> I want to store partial atomic charges for periodic structures
>> and load them into jmol for visualization purposes. Does anyone know
>> the simplest file format to accomplish this?
>>
>> I know that partial atomic charges can be stored in an xyz file format.
>> Does anyone know whether periodic lattice vectors can also be
>> placed in an xyz file format and loaded into jmol.
>> If so, does anyone know where I could obtain a sample file of a
>> periodic structure in xzy format that can be read by jmol?
>>
>> Sincere thanks,
>>
>> -Tom M.
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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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