Re: [Jmol-users] Supercell and autocompletion of fragments

[Robert H. <ha...@st...>]

On Fri, Aug 1, 2014 at 3:21 PM, Michael F. Peintinger <
mic...@gm...> wrote:

>  Dear Bob,
>
> thank you for your quick reply.
> Sadly the command did not work properly,
> the outermost molecules are incomplete.
> I helped myself by creating the supercell
> a priori with CRYSTAL.
> Then I load it from the output and complete with:
>
> load "" {444 666 1};display within(molecule, cell=555);
>
> On the screen, everything looks fine.
> I then call
> delete hidden
> to remove the hidden atoms.
>
> But when I try to export it to a xyz file:
> write XYZ "cluster.xyz"
> There are too many atoms in the xyz file.
> It looks like there are several molecules
> remaining from the auto complete.
>
> How do I get JMol to write only the atoms
> that are actually on the screen?
>
>
select visible

then do the write command


> I am using JMol 14.2, should I downgrade
> to a stable release?
>

no, no. That's a good one.. And it is the stable release.
14.3 is the development version. I hope to synchronize them
tomorrow.

Bob

>
> All the best
>
> Michael
>
>
>
> On 01.08.2014 16:19, Robert Hanson wrote:
>
>
>
>
> On Fri, Aug 1, 2014 at 9:14 AM, Michael Florian Peintinger <
> mic...@gm...> wrote:
>
>> Dear all,
>>
>> I use the following command to auto-complete molecular fragments
>> that extent to the outer side of the unit cell:
>>
>> load "" {444 666 1};display within(molecule, cell=555);
>>
>> What I would like to do now is to create a supercell and then
>> use this supercell for the auto-completion.
>>
>> I tried combinations like:
>> load "" {1 1 1} supercell {3 3 1};display{666 444 1};display
>> within(molecule, cell=555);
>>
>
>
>  load "" {444 666 1} supercell {3 3 1}
>  display within(molecule, cell=555);
>
>
> should work.
>
>
>> Thanks
>>
>>
>> Michael
>>
>>
>> --
>> Dr. Michael F. Peintinger
>>
>> http://www.peintinger.com
>>
>> MPI für Chemische Energiekonversion
>> Abteilung für Molekulare Theorie und Spektroskopie
>> Stiftstrasse 34 - 36
>> D-45470 Mülheim an der Ruhr
>>
>> http://cec.mpg.de
>>
>> Tel.: +49 (0)208 306 - 3584
>> Fax : +49 (0)208 306 - 3951
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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
>
>
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.http://p.sf.net/sfu/bds
>
>
>
> _______________________________________________
> Jmol-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> --
> Dr. Michael F. Peintinger
> http://www.peintinger.com
>
> MPI für Chemische Energiekonversion
> Abteilung für Molekulare Theorie und Spektroskopie
> Stiftstrasse 34 - 36
> D-45470 Mülheim an der Ruhr
> http://cec.mpg.de
>
> Tel.: +49 (0)208 306 - 3584
> Fax:  +49 (0)208 306 - 3951
>
>
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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