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

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 @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.

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

Dear @Lauren ,

We have updated the Creating visualizations: Van der Waals visual model tutorial in our Developer Guide.

You can also check out the code samples corresponding to this tutorial here: https://github.com/1A-OneAngstrom/SAMSON-Developer-Tutorials/tree/master/VanDerWaals. The code samples contain more optimized code and some additional functionality.

Great! Thanks for the reply.

Please do not hesitate if you have more questions.

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?

Ok thanks. I'm going to contact you by email for further exchange.

@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?

there is RMSF and hydrogen bond

I have a structure I would like to alter a bit using Adenita, but whenever I try to select it, it becomes non-responsive and crashes. I've tried using a .json file and a .pdb file and neither is capable of having parts selected. I tried on two different computers, one with a quad-core and one with a 6-core and it still crashed. Is there a way I can perform this on my build? Or is this a software issue that others experienced?

OS: Windows 10
Ver: SAMSON 0.8.5

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.

Great! Thank you for your reply!

Dear Sebastian,

one possibility might be to ask the Vina extension to compute many modes (e.g. 1000) and then use a script to filter out the conformations that do not satisfy the distance constraint. Another possibility might be to directly modify the source code of Vina to add a term to the scoring function that would penalize one or more unsatisfied constraint(s) (similar to a NMR energy function). We're going to look into this. Thanks for the suggestion.

Best,

Stephane

Thanks this is very good to know