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J-Ice: Interface for crystal (Read 3887 times)
Gerrit-Jan Linker
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J-Ice: Interface for crystal
15.09.11 at 08:01:41
 
J-Ice: Interface for crystal
 
 
J-ICE is an Interface for Crystallographic and Electronic properties. It can read outputs from crystal (and other programs) and view the results. It is great to visualise geometry optimisations, geometries, vibrational frequencies, and more!
 
http://j-ice.sourceforge.net/
 
J-ICE is using the JMol package. For JMol see:
http://chemapps.stolaf.edu/jmol/docs/
 
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« Last Edit: 19.05.12 at 09:02:51 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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J-Ice / JMol commands
Reply #1 - 13.09.12 at 10:43:16
 
J-Ice / JMol commands
 
Some commands to edit a structure:
 
Move atoms in fractional coordinates:
Select atoms (so the halo is visible)
In the console window type:
translateselected -1/1 1/1 0
The / indicate fractional coords. This command translates along -a +b 0
 
Delete atoms:
Select atoms
In the console window type:
delete selection
 
Increase the selection of atoms by adding other atoms within a sphere of 2 Angstrom:
Select some atoms
In the console window type:
select within(2,selection)
 
Draw arrow:
draw mylabel arrow {0 0 0} {0 1 0}
 
Add a label:
set echo mylabel {0 0 1}
echo "Hello World"
 
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« Last Edit: 27.09.12 at 13:08:36 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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Re: J-Ice: Interface for crystal
Reply #2 - 27.09.12 at 13:11:43
 
J-Ice/Jmol examples
 
Quote:
background red;
data "model example"
2
testing
C 1 1 1
O 2 2 2
end "model example";show data
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Gerrit-Jan Linker
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J-Ice: JMol useful commands
Reply #3 - 03.04.13 at 21:54:43
 
J-Ice: JMol useful commands
 
>print {atomno=1}.molecule
1
>select molecule=1
>display molecule=1
 
>delete within(molecule,atomno=364)
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« Last Edit: 03.04.13 at 22:10:38 by Gerrit-Jan Linker »  

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