Another possibility could be to start from a selenium crystal and "sculpt it".
Get a CIF file for a crystal you like at
http://rruff.geo.arizona.edu/AMS/minerals/Selenium. You will need the CIF importer in the Crystal Creator SAMSON Element (
https://samson-connect.net/app/main?key=element&uuid=58a75a78-abbc-2c60-6214-e668b5c45a0d). In this example, I'm using this CIF file:
http://rruff.geo.arizona.edu/AMS/download.php?id=10390.cif&down=cif.
When you import the CIF file, use a big enough number of cells, for example 10 in each direction:
This will create 32000 atoms:
Select one atom around the center of the crystal, with the selection editor :
(look around to make sure the selected atom is approximately in the center)
Open the Find window (CTRL / CMD + F or Selection / Find...):
Enter the following search string: n.t a w 20A of n.s in the box named "Selection string" and press the OK button. This is the short form of "node.type atom within 20 Angstrom of node.selected", i.e. all atoms within 20A of the current selection. This selects atoms in a 20A radius sphere:
Open the Find window again, to invert the selection with the following NSL expression: n.t a and !n.s (in the box named "Selection string", then press OK). This means "all nodes that are atoms and that are not selected". This selects everything outside the nanoparticle:
Press the "delete" key to erase the selected atoms, or click on the "Current selection" widget and select "Erase selection":
This leaves the particle alone:
In the Document view, select the Property model called "Selenium crystal" and delete it, i.e. go from
to
You now have a spherical selenium nanoparticle with a 20A radius. Save it to a SAMSON file format or export it to a PDB file. Here is the SAMSON version:
0_1528386144295_Selenium nanoparticle.sam
Hope this helps,
Stephane
