Getting started

Hi @Dheeraj-0 , Unfortunately, we discontinue support for older versions of SAMSON, so we cannot recommend or provide an older compatible version. If possible, we suggest trying the latest version of SAMSON on a newer machine that supports macOS 13 or later. Sorry for the inconvenience, and thank you for your understanding.

@Jocelyn Hi, It's GNOME Shell 48.5 Thanks.

The groups on the SAMSON Connect website are mainly for collaboration purposes (see: User Guide: Collaboration), but they can be extended to manage licenses.

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

You don't need to upgrade your whole system; you can try to update it via the above-given commands which will update the packages installed on your system. And if glibc 2.33 is not available with the update you can try to install it from OpenSUSE Tumbleweed.

Possibly, it is not supported with Cycles kernels (from Blender's Cycles) that we ship. We will try to see what we can do here. Or, maybe, the Cycles kernels we ship are not compatible with the CUDA version installed on your OS.

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 @AntiDown , Ok. I am glad it works for you now. Thank you for your reply!

Great! I am glad that it worked! Do not hesitate to contact us if you have any questions or feedback.

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: [image: 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

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

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,

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: [image: 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: [image: 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: [image: 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.

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