Hi Melisa, There are many structures that are only partially protonated, so the fact that your structure has hydrogen atoms does not prevent ChimeraX from thinking that some hydrogens could be missing. That's what's happening in this case. ChimeraX believes that the epsilon nitrogen of the histidine should be protonated. Looking at the geometry of the two nitrogens and their distance, it would be somewhat surprising if the epsilon nitrogen wasn't protonated, because it is completely ideal for a hydrogen bond. If you ran "addh", ChimeraX would add a proton to the epsilon nitrogen. At any rate, if you have some evidence that the epsilon nitrogen isn't protonated, you can prevent ChimeraX from thinking that it is by changing the atom type of the epsilon nitrogen with this command: setattr /A:163@ne2 a idatm_type N2 --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 15, 2024, at 12:23 PM, Melisa Kalaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello. I wanted to display the hydrogen bonds between my ligand and protein, however when I hovered over the displayed bonds with my cursor I noticed one of the bonds being between two nitrogen atoms and I was confused. Is this a bug within the software? I'll attach a screenhot so you can take a look at it yourself: https://drive.google.com/file/d/1N5YRncOrrJnEVRpM8XD7O1tPG02ZTu8G/view?usp=d... _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/