SAMSON

Hi @Federico-Maria , We have modified the behavior of the importers - they should not create covalent bonds for metal coordinations. It previously considered all connections described in the file as covalent ones. The corresponding modules will be updated automatically for you once you restart SAMSON.

Dear @Ricardo-2 , Due to policy updates, we no longer support older versions of SAMSON and have removed them from access. Could you please tell us which features are missing for you in the latest SAMSON and which version of SAMSON you want to install?

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.

Great video, Tom! Thanks for posting it!

Hi, Did you perform other steps (preparation, minimization, equilibration) in GROMACS Wizard before running the production MD (see GROMACS Wizard tutorials)? If not, you might want to try to run them starting from the preparation step. Could you share the input (all the input files for the step) and resulting files (the corresponding folder into which GROMACS Wizard saved the resulting files, named with a time stamp, e.g. "2024-10-23_09h55m26s-simulate-error") with us so we can try to reproduce the issue and see is the problem?

thank you

Dear @Luis , Great! Thanks for checking and for reporting the issue in the first place!

Currently, there is no public extension in SAMSON that can launch/use LAMMPS. But you can export your system into a LAMMPS Data format and load LAMMPS files (data and trajectories) back in SAMSON. We plan on adding the support for periodic boundary conditions in one of the future releases of SAMSON. For some systems, you can simulate without PBC or by freezing the boundary atoms to fix them. You can also combine simulations in SAMSON with e.g. ASE package using Python, see Python scripting: Combining SAMSON simulation with ASE calculators

Dear @Mattia-Felice , Thank you for the feedback! We will consider this for the next releases of SAMSON. We will surely add more labeling possibilities in the next release. As for formats from ab initio packages, SAMSON currently supports only Molden and it loads only the molecular structure from it. But we can add the possibility to load other data from it as well.

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) [image: 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.

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!

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.

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!

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: [image: 0_1612374085845_ce0855be-0ca8-49e4-a8fd-bbf45f42f1b6-image.png] Could you please let me know if this works for you?

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

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

Okay, Thanks.