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