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 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

Dear @Artyom ,

The file is loaded ok. The model and the selection (in orange) are partially hidden by the Fog effect. You can switch off the Fog effect in the Visualization menu > Effects > Fog or modify the Fog parameters in the Preferences (Ctrl/Cmd + K) > Rendering > Fog - set the far distance to 100 A, for example.

You can also check out the User guide: Preferences and User guide: Visualizing documentation.

Gaussian surfaces may be slow to recompute sometimes (e.g. for large molecules), so there is an "Update" button to recompute the surface. You need to use it when you change the color.

About the transparency: it depends on the order of visual models. Since order-independent transparency is not yet implemented, you will see the secondary structure only if it comes before the gaussian surface (when you traverse the document in depth-first order).

Here is an example with the Gaussian surface first:
0_1512040615642_GSS.png

And here is an example with the Gaussian surface after the secondary structure:
0_1512040385013_SSG.png

Dear @Tanish ,

Adenita is a third-party extension developed by external developers. Since it is open-source, we started porting it ourselves to the latest SAMSON. The latest SAMSON compared to the versions of SAMSON which support Adenita has a lot of major changes meaning that the porting process will take quite some time especially together with fixing some issues in Adenita. Currently, we cannot give a time estimate since we work on it occasionally in our free time, but we hope it will be ready in the upcoming months.

We are sorry about the inconvenience.

Dear @Oisin ,

Covalent bonds are created based on the interatomic distances. Maybe the atoms are placed too far from each other? Could you please check the distance between atoms in your system - you can do it using the Measure editor by clicking on two atoms consecutively. Could you please attach a .cif file in which you experience the problem such that we could check it.

By the way, are you referring to .cif for biomolecules (mmcif/PDBx format) or .cif for crystals?

@martin-1

Dear Martin,

Thanks for your feedback. It appears you’re on a very specific machine as most users install SAMSON within minutes without any issues on Windows Linux or Mac in standard directories. Please contact the developers at contact@samson-connect.net as indicated in the automated email you received about installation.

We’re happy you think SAMSON is looking good too :).

Best

Hello, high-resolution displays are not supported natively yet, but Windows 10 indeed allows you to change the settings. On my 4K monitor, I use the method explained there : https://blog.pauby.com/post/high-dpi-settings-windows-10/ , but I choose "System" instead of "Application". My system DPI adjustment is at 200% in Windows, and here is how it looks like:
0_1612374085845_ce0855be-0ca8-49e4-a8fd-bbf45f42f1b6-image.png

Could you please let me know if this works for you?

Dear @Olivia ,

The Adenita extension has been developed and is supported by external developers ( @Elisa ). And Adenita is in an alpha stage and might have some issues. We plan on porting this extension to the most recent SAMSON version.

You can also copy your question to the specific topic: Adenita - User Support.

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

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

Hello, could you please tell us which graphics card you have? This seems to indicate a GPU issue.

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

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.

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).

Hi Clement,

To listen to the document closed signal I connect my nodes to a custom signal like this:

SB_FOR(SBNode* node, atomIndexer) node->connectBaseSignalToSlot(this, SB_SLOT(&SENormalModesAnalysisApp::onBaseEvent));

Then, in my onBaseEvent function I catch the NodeEraseBegin event which corresponds to the signal emitted when the document is closed or the nodes erased.

void SENormalModesAnalysisApp::onBaseEvent(SBBaseEvent* event) { if (event->getType() == SBBaseEvent::NodeEraseBegin) { //disconnet the connected nodes SB_FOR(SBNode* node, atomIndexer) {node->disconnectBaseSignalFromSlot(this, SB_SLOT(&SENormalModesAnalysisApp::onBaseEvent)); } //....// }

Remember to disconnect the connected nodes.
Hope I answered your question,
Yassine

Hello Arturo,

thanks for your interest in SAMSON!
The AutoDock Vina element has been deprecated as it was offering limited functionality (only one ligand at a time). It is still possible to use the AutoDock Vina Extended element for free for 30 days (no credit card needed) and it can do more, including pre-minimization of ligands and docking entire libraries.
Can you please ask your teacher to contact us at contact@samson-connect.net so we can find the best solution to provide access to all students?

Thanks,
Stephane

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.