Great! Thanks for letting us know.

Hi Pedro,

We're sorry about the issue.

Could you please try to delete the following folders:

(IMPORTANT: make sure you don't have e.g. personal SAMSON documents in these folders that you might want to preserve.)

C:/Users/[USERNAME]/AppData/Local/OneAngstrom/
C:/Users/[USERNAME]/OneAngstrom/
C:/Users/[USERNAME]/Documents/OneAngstrom/

and try to reinstall SAMSON to see what happens?

Maybe there is a need to specify in your Windows settings that SAMSON should use specifically the NVIDIA GPU ? Please let us know.

Dear @Filipe

Normally it should be rendering double bonds by default, but you can change this setting in Preferences > Rendering > Structural models - check the Render multiple bonds option:
5d539e47-b05e-4872-8cc1-d1d36cb34dc5-image.png

As for the PBT format, currently, SAMSON does not have the PBT format exporter, but you can export in OBJ or glTF formats for use in Blender.

Best,
The SAMSON Team

Great contribution!

Hi @albert ,

There are several options for the colorization of structures or visual models (Ribbons is a visual model) based on chains:

The colorization using color schemes. First, select the Ribbons visual model in the Document view that you would like to colorize. Then: Biology > Colorize > Chain ID or Chain (illustrative) (i.e. in the style of D.S.Goodsell)
aedf2d1e-77e3-42cd-af72-51400ba6f73b-image.png
You can also choose "Custom..." from the list and specify the color palette. The colorization with constant colors per chain. Choose a chain in the Document view. Set the color using Visualization > Colorize.

See more in User guide - Colorizing and User guide - Visualizing.

Dear @Zilong

It’s not currently possible to export vector images. However, you can change the image resolution in the preferences:

Open the Preferences (Menu Interface > Preferences) In the Preferences, go to Interface > Captures to change capture settings, including the resolution.

Great! Thanks Tom!

Thanks Tom!

Dear @Tom-1 ,

We have added an example of how to build molecules using Python Scripting in SAMSON, please see SAMSON-Python-Samples > building.

Please let us know if you have any questions or feedback.

Dear @闽乐 ,

In the new version, you can access the control parameters for the visual model via the Inspector. For that, simply select the Adenita visual model and open the Inspector - you can right-click on the Adenita visual model and choose Inspect in the context menu.

See: User guide - Inspecting

Dear @Elsaid ,

This happens because of the Wayland display server on Ubuntu. You can try specifying another display server.

If you launch SAMSON from a terminal, then you could first specify the environment variable QT_QPA_PLATFORM to use the Xorg display server (X11):
export QT_QPA_PLATFORM=xcb

Then start SAMSON in the same terminal. Note, SAMSON is installed in your home directory ~/OneAngstrom/SAMSON-Application/4.0.0/Binaries, you can try starting ./SAMSON-Launcher.sh

If this works, you can try disabling Wayland on your system, for that you will need sudo privileges:

Disable Wayland by uncommenting WaylandEnable=false in the /etc/gdm3/custom.conf Add QT_QPA_PLATFORM=xcb in your ~/.bashrc file.

You might need to restart either the OS or the terminal.

You can check whether your system uses Wayland or X11 by running the following command in the terminal:
echo $XDG_SESSION_TYPE

Hi Chris, thanks again for reaching out! As discussed, this was caused by having ligands with multiple connected components, which Vina cannot dock. We will try to provide clearer error messages to prevent this. Thanks again!

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,

Wonderful, thanks for the tip. It took a little adjustment for me to get familiar with Inspector to just show the new model without the C-H's, but this works well.

Dear @Eva ,

We have improved the performance of surface visual models (Gaussian, Solvent Accessible, and Solvent Excluded surfaces) in certain cases. For example, now animations with them should be much faster. The visual models should be automatically updated for you once you restart SAMSON.

Awesome, thanks for letting us know!

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

Dear Elsaid,

we just released an update of the editors which makes it possible to use the current selection to build. This should make it easier to build any polymer you want by repeatedly adding larger and larger groups.

When using the Rectangle selection editor (the default editor, shortcut R), show the context menu (either by right-clicking in the viewport, right-clicking in the Document view, or clicking the green selection widget in the Document view). The third context menu action is Use selection to build:
0_1644692016713_e83ed7a6-57d6-44ce-99d0-73bb958e632c-image.png

Clicking this action automatically switches to the Add editor ands use the selection as a building fragment:
0_1644692230894_100a0c07-d9ca-47c3-9a78-4f6e322c4ad1-image.png

The Use selection to build action is also available in the context menu when the Add editor (shortcut A), Edit bonds editor (shortcut B) and Edit charges editor (shortcut C) are active. Here it is for example in the Add editor:
0_1644692355053_01b3ea45-9fe8-4584-8676-2fcb433572e6-image.png

Best regards,

The SAMSON team at OneAngstrom

Hi Luis, sorry for the delay! Could you please contact us at contact@samson-connect.net? It would be easier to chat / zoom about this so we can focus the development.
Thanks!
best,

Stephane