how to draw the picture using the VNL?

[qnsyhanjiu]

When I draw the picture use the vnl,how to make the molecule's key to join and how to change the molecule's color? Thank you! I wish to I receive a good answer. This system is two-probe.

[zh]

The atomic coordinates of atoms in the two-probe system can be printed out in the unit of angstrom using "nlprint()". So you can write these atomic coordinates into a file in the XYZ format, visualize the geometry using VESTA (http://www.geocities.jp/kmo_mma/crystal/en/vesta.html) or XCrySDen(http://www.xcrysden.org/), and adjust the color of atom (or other actions).

[Anders Blom]

In VNL 11.2 (and 10.8 ) it is actually possible to change the color of individual atoms. You just select them (in the Viewer), then right-click and choose "Colors" from the context menu. As you see then, you can also change opacity, radius, etc of the selected atoms. Note that all selected atoms will be given the same color when using this operation.

[qnsyhanjiu]

Dear zh,
    How I can make the file into a xyz? Thank you! For example,how can I make a .py into .xyz?

[Anders Blom]

In the Builder you can File>Export a structure to an XYZ file.

[qnsyhanjiu]

In the vnl,how I can make the .py to into .xyz? That is my vnl in the additional options.

[zh]

If you use the version of ATK2011, the xyz file of a configuration can be exported using the options "File--->Export Configurations....---->Files of type" in the "Builder" tool, as mentioned by Anders Blom.

Since you used the version of ATK2008,  the xyz file can not be exported in the above manner. It can be done in a complicated manner:
1). transfer the configuration into to the "Script Editor". In the window of "Script Editor" for you configuration, add the following line at the end of the nanolanguage script:
nlPrint(the name of your configuration)
2). drag the script file in the 1st step onto the "Job Manager";
3). the atomic coordinates will be printed out in the log file. Copy them into an ascii file, edit it according to the XYZ file format and then save it as a xyz file.