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?
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 email@example.com as indicated in the automated email you received about installation.
We’re happy you think SAMSON is looking good too :).
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:
Could you please let me know if this works for you?
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?
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.
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.
To find and show hydrogen bonds you can use the Hydrogen Bond Finder Extension. It allows you to find all H-bonds in the selected system or between two systems, for example, between a receptor and a ligand.
To find/show H-bonds between a receptor and a ligand, perform the following steps (see the gif at the end):
Alternatively, you can do this without the Brenner interaction model but with the built-in minimization which uses the Universal Force Field (UFF) and the Add editor (shortcut: A) (it's Carbon by default).
First, you will need to modify SAMSON preferences (Ctrl+K):
-1- For the Add editor, disable the "Adjust hydrogens ..." option.
-2- For the Minimization, disable the "Warn me when hydrogens appear to be missing" warning to prevent it from poping-up on each new bond connection.
Then you can apply the minimization: Home >Simulate > Minimize. Start connecting atoms in the nanotube and the graphene sheet using the Add editor (A) - to create a bond simply connect two atoms with this editor.
The error message ("atom N not found in buiding block 1ACE while combining tdb and rtp") suggests that, in your model, 1ACE contains a N that should not be there (according to GROMACS topologies). You might have to remove it, or move it to the next residue. You can reorganize atoms, residues, etc. easilyby just dragging nodes around in the Document View.