No way for now, thanks for the idea :).

Thanks for the replies, Dmitriy and Stephane.

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:
0_1528385266091_08798f27-b8d7-4139-8e87-97f67c07b32f-image.png
This will create 32000 atoms:
0_1528385319471_d2cb857d-3ff4-4d2f-ba1b-9f52e0170c30-image.png Select one atom around the center of the crystal, with the selection editor 0_1528385357394_dd40b047-a00b-4346-8801-e0193268107e-image.png:
0_1528385397414_315ea865-a94f-4f62-a4be-8348071ee4e0-image.png
(look around to make sure the selected atom is approximately in the center) Open the Find window (CTRL / CMD + F or Selection / Find...):
0_1528385478242_d43a3244-962b-4bcd-94f1-4ea3c052fe58-image.png 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:
0_1528385607949_e9280e37-b54c-4560-9e6a-133282b1f0bc-image.png 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:
0_1528385806987_1.png Press the "delete" key to erase the selected atoms, or click on the "Current selection" widget and select "Erase selection":
0_1528385902405_a3c8d30d-c47e-41ed-a5da-5d9a307eb47c-image.png
This leaves the particle alone:
0_1528385954376_7e5484ab-1bb4-44b0-8d96-f6534eb60b9d-image.png In the Document view, select the Property model called "Selenium crystal" and delete it, i.e. go from
0_1528386023100_d66cd933-e574-4c80-bbc9-35c1820851ee-image.png
to
0_1528386038473_4a83e287-d616-4cbb-ad50-695cc3fd846d-image.png 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

Thank you, Dmitriy. I will try later. I just tried to open pdb file in Windows, and in status bar got the message, that it "can''t open" my file. I will try to put the log here a bit later.

Ah ok good. Yes SAMSON determines which importer to use based on the file extension.

Hello, when using the installer, you can check the box "Install older versions". The next step will give you the possibility of choosing the version you want, including 0.7.

Thank you @Rahad !
Do you mean the minimization step in the AutoDock Vina Extended module? What error does it show?

As for ligand libraries, AutoDock Vina Extended module supports libraries with ligands in formats that can be opened in SAMSON, including .pdb, .mol2, .sdf, .xyz, etc, but not .mol and .pdbqt for now. You do not need to import all the ligands in SAMSON, you just need to provide the path to the folder with a ligand library.

Yes, I could already run it.
Thank you!

@emmanuel
For now, you can just reapply the Hydrophobicity color scheme (Biology menu > Colorize > Hydrophobicity).

Currently, it is not possible because the selection filter functionality is not exposed to external elements. We will update it in the upcoming release of SAMSON.

Adenita needs older versions of SAMSON because it hasn’t been updated yet (you can see this on the element page). You need to reinstall SAMSON and check the box “Install older versions” to install 0.8.5. Also, please check the requirements on the element page.

Thanks Dear.

Thanks for reporting this bug! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed this monday (may 11, 2020).

Dear @Emmanuel ,

Thanks for reporting this issue! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed in a few days.

Dear @Emmanuel ,

Thanks for reporting this issue! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed in a few days.

Thank you @Emmanuel for reporting these issues. We have fixed them - the Elements will be updated automatically once you launch SAMSON.

Okay, Thanks.

Hi James, thanks for reporting this. We sent you an email to determine the issue.