Hi Joshua,
Chimera is just measuring the distances in the data files that you gave it.  It is not setting (changing) them unless you are changing the structure yourself manually.  All I can say is that hydrogen is small, so its closest interactions may be at shorter distances than some covalent bonds between bigger atoms.   You can look up expected lengths for all kinds of bonds (covalent and H-bonds) in the literature and probably also protein structure textbooks.
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 16, 2024, at 7:14 PM, Joshua Angelo Mandanas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Greetings from the Philippines!
>
> Hi, I am Assoc. Prof Joshua Angelo, a Lead Researcher.
>
> I am currently utilizing Chimera to analyze/visualize the docked structures I processed in ClusPro.
>
> In the course of my utilization with Chimera, I came across that majority of hydrogen bonds have closer atomic interactions (e.g. 1.8 Å- 2.5 Å), as opposed to covalent bonds (I usually get atomic distances more than 2.5 or 2 Å). Note, that I based the covalent bonds based on the label from the atomic distance and nature of the residues involved (e.g. S-O, C-O).
>
> I humbly would like to know why covalent bonds in UCSF Chimera have further atomic (residue) distances between inter-models? Is it because of torsions from nearby hydrogen bonds? Or torsions from the actual docked structure?
>
> Hope for your prompt response. Thank you very much!
>
> Best regards,
>
> JOSH