[Jmol-users] How can i show the total molecule tegether in JMOL? Thanks.

2010-02-01 Thread houyang chen
Hello, everyone,

I got a result of molecules coordinates from simulation.
When i shown it by JMOL, i found part of molecule is in the left side of x
axis in the box; and the other part
is in the right side of x axis in the box.
This is cause by the period bound condition in the simulation.
How can i show the total molecule tegether in JMOL?

Thanks.

Houyang
--
The Planet: dedicated and managed hosting, cloud storage, colocation
Stay online with enterprise data centers and the best network in the business
Choose flexible plans and management services without long-term contracts
Personal 24x7 support from experience hosting pros just a phone call away.
http://p.sf.net/sfu/theplanet-com___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


Re: [Jmol-users] How can i show the total molecule tegether in JMOL? Thanks.

2010-02-01 Thread Robert Hanson
What sort of file is it?

You need to load the file with symmetry and unit cell and load more than one
unit cell. Something like:

 load caffeine.xyz {1 1 1} spacegroup P1 unitcell 10.0 10.0 10.0 90 90
90

However this does not work with all file types. But that can be fixed...

Bob


On Mon, Feb 1, 2010 at 2:45 PM, houyang chen houyangc...@gmail.com wrote:

 Hello, everyone,

 I got a result of molecules coordinates from simulation.
 When i shown it by JMOL, i found part of molecule is in the left side of x
 axis in the box; and the other part
 is in the right side of x axis in the box.
 This is cause by the period bound condition in the simulation.
 How can i show the total molecule tegether in JMOL?

 Thanks.

 Houyang


 --
 The Planet: dedicated and managed hosting, cloud storage, colocation
 Stay online with enterprise data centers and the best network in the
 business
 Choose flexible plans and management services without long-term contracts
 Personal 24x7 support from experience hosting pros just a phone call away.
 http://p.sf.net/sfu/theplanet-com
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




-- 
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
--
The Planet: dedicated and managed hosting, cloud storage, colocation
Stay online with enterprise data centers and the best network in the business
Choose flexible plans and management services without long-term contracts
Personal 24x7 support from experience hosting pros just a phone call away.
http://p.sf.net/sfu/theplanet-com___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users