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 <michael.peintinger@gmail.com> 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


------------------------------------------------------------------------------
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
Jmol-users@lists.sourceforge.net
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



------------------------------------------------------------------------------
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
Jmol-users@lists.sourceforge.net
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