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

First of all I have to thank you for the quick response. Funnily, I thought of using const_cast on the matrix pointer beforehand but considered it as too "hacky".
There should be several possibilites how one could introduce this into the API:

Each camera gets a state that determines whether it implements a symmetric or asymmetric projection including two methods that query and set the state. Then, an additonal method (possibly like SetPlanesAsymmetric(float left, float right, float top, float bottom)) could be used to transfer the wanted plane values to SAMSON. This approach would leave the old API intact, if the symmetric projection is the standard state. Derive a class like SBDAsymmetricDocumentCamera from the currently available SBDDocumentCamera, overriding all methods concerning the projection matrix. This is probably the least favourable alternative, although the old API would still be valid. The camera gets two additional methods SetValuesSymmetric(float aspect, float fovy, float zNear, float zFar) and SetValuesAsymmetric(float left, float right, float top, float bottom, float zNear, float zFar). Then, the GetProjectionMatrix() and GetProjectionMatrixTranspose() methods would have to be changed to take an additional boolean input parameter determining which kind of matrix is wanted. This would break the old API and I am not sure how this would propagate to the convenience display methods like SAMSON::displayCylinders(...).

Unfortunately I do not know which of these possibilities (and I probably missed some additional ones) would fit best into your way of writing SAMSON.

Best,
Karsten

Thank you so much sir....It really helped.

yes you are right both ways work fine.
I had a bug I was unaware of in a different position.

thx!

Actually I didn't explain well the case where the raise didn't worked for me as I expected. When you have two windows, with the first one locked and the second unlocked. If the raise function is called for the second unlocked window, it doesn't go on top of the first locked window.

For those who might interest, I found a simple solution. You need to temporarily lock the window, call the raise function then unlock the window.

Thank you Stephane for your quick answer !
Yassine

@stephane-redon I think it can be nice for the developers to be able to register more actions in the context menu. But it can also make the context menu too crowded. Perhaps, you can make something in the Preferences so that the users can select to add which actions to show in the context menu.

Actually, I am developing an app to convert a list of conformations to a path and vice versa for my work.
So I was thinking it can be useful to add an action in the context menu so that after selecting a list of conformations in the Document View, I would right-click and choose "Convert to Path". Do you have any suggestion to do it for this case?

Yes thanks. That's what I was looking for.

Hi @Stephane-Redon,

ah yes, it was the depth test. This solves it!

Thanks,
Haichao

We have posted a brief tutorial on preparing protein-ligand systems with GROMACS Wizard. We will add more information to it over time, specific to each parametrization tool/server.

Dear Michael,
I fixed the issue in the GROMACS importers (trajectories, .gro) on macOS that was causing the options to be disabled and was also affecting the GROMACS Wizard. Could you please check whether the GROMACS Wizard and loading of GROMACS trajectories now work for you?

Not instead, in addition: having, at the installation of the App, a list of pre-saved settings, with still the possibility to save and load your own settings.
-- for example, with the Crystal Creator App, having the 'diamond settings', the 'SiGe settings', or for ARPS, some classical configurations of Ef and Er : the '10x speed up settings', '5x speed up settings' ... --

Hi @John-4 ,

In the first Python script you showed, the LLM you used (did you use Gemini or SAMSON's AI Assistant?) hallucinated and used some non-existent libraries, classes, and functions in SAMSON, which resulted in errors.

Ok, got it. SAMSON is a high priority application, so on C: it goes.

Dear @Dominic ,

We've just updated the Adenita extension: it now sets the nucleotide names as expected by PDB - DA, DC, DG, DT. Now, it should be suitable for export in the PDB format.

Dear @Grigorii ,

Yes, currently, Adenita does not serialize/save its visual model when saving into a file. You need to reset it via Adenita.

Dear 闽乐 ,

We have fixed some possible issues in Adenita - it should be updated automatically for you. Could you please check whether it works for you?

Hello,

Although I have re-install Ubuntu with 200GB mounted in /, it still stoped around 29

When I run %df -l, it showed below

Filesystem 1K-blocks Used Available Use% Mounted on
udev 131770300 0 131770300 0% /dev
tmpfs 26361104 2888 26358216 1% /run
/dev/nvme0n1p2 191197068 11936596 169478456 7% /
tmpfs 131805512 46716 131758796 1% /dev/shm
tmpfs 5120 4 5116 1% /run/lock
tmpfs 131805512 0 131805512 0% /sys/fs/cgroup
/dev/loop0 9216 9216 0 100% /snap/canonical-livepatch/132
/dev/loop2 289280 289280 0 100% /snap/pymol-oss/98
/dev/loop1 113280 113280 0 100% /snap/core/12834
/dev/loop3 33152 33152 0 100% /snap/snapd/12704
/dev/loop4 63488 63488 0 100% /snap/core20/1405
/dev/loop5 66688 66688 0 100% /snap/gtk-common-themes/1515
/dev/loop6 254848 254848 0 100% /snap/gnome-3-38-2004/99
/dev/loop7 56832 56832 0 100% /snap/core18/2128
/dev/loop8 224256 224256 0 100% /snap/gnome-3-34-1804/72
/dev/nvme0n1p3 758522328 506548 719415232 1% /home
/dev/nvme0n1p1 9755312 5384 9749928 1% /boot/efi
/dev/nvme1n1p1 960379920 77856 911447640 1% /home2
/dev/loop9 52224 52224 0 100% /snap/snap-store/547
tmpfs 26361100 20 26361080 1% /run/user/125
tmpfs 26361100 44 26361056 1% /run/user/1000

I think it is not a space problem though, I don't know how to solve this problems.

please help,

Great, thanks! I will also mess with transparency, etc. in order to see some interactions in more detail.

Thank you for your quick response, it is much appreciated!

Hi Nick, thanks for the posts, we've sent you messages about how to reach us for chat so we can help you.