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?
I am using JMol 14.2, should I downgrade
to a stable release?
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
> <[email protected] <mailto:[email protected]>>
> 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 <tel:%2B49%20%280%29208%20306%20-%203584>
> Fax : +49 (0)208 306 - 3951 <tel:%2B49%20%280%29208%20306%20-%203951>
>
>
>
> ------------------------------------------------------------------------------
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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 list
> [email protected]
> 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
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